# HG changeset patch
# User iuc
# Date 1544809639 18000
# Node ID cdd90678004a78d89816f5470c3909e90f3ffbed
# Parent  ee894347fcd62d19e4085f1dc20a6e0625211cc0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

diff -r ee894347fcd6 -r cdd90678004a gemini_macros.xml
--- a/gemini_macros.xml	Wed Oct 17 13:33:53 2018 -0400
+++ b/gemini_macros.xml	Fri Dec 14 12:47:19 2018 -0500
@@ -1,7 +1,12 @@
 <macros>
+    <!-- gemini version to be used -->
+    <token name="@VERSION@">0.18.1</token>
+    <!-- minimal annotation files version required by this version of gemini -->
+    <token name="@DB_VERSION@">181</token>
+
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.18.1">gemini</requirement>
+            <requirement type="package" version="@VERSION@">gemini</requirement>
             <requirement type="package" version="0.2.6">tabix</requirement>
             <!-- for conda useage -->
             <!--requirement type="package" version="1.3.1">htslib</requirement-->
@@ -23,9 +28,10 @@
     </xml>
 
     <xml name="annotation_dir">
-        <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
-            <options from_data_table="gemini_databases">
+        <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
+            <options from_data_table="gemini_versioned_databases">
                 <filter type="sort_by" column="0" />
+                <filter type="static_value" column="2" value="@DB_VERSION@" />
             </options>
         </param>
     </xml>
@@ -97,6 +103,12 @@
        </sanitizer>
     </xml>
 
+    <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
+        mkdir gemini &&
+        ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
+        export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
+    ]]></token>
+
     <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
         #set $sql_expr = str($multiline_sql_expr).strip()
         #if str($sql_expr):
@@ -153,7 +165,6 @@
     <xml name="gt_pl_max">
         <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
     </xml>
-    <token name="@VERSION@">0.18.1</token>
 
     <xml name="citations">
         <citations>
diff -r ee894347fcd6 -r cdd90678004a gemini_stats.xml
--- a/gemini_stats.xml	Wed Oct 17 13:33:53 2018 -0400
+++ b/gemini_stats.xml	Fri Dec 14 12:47:19 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
     <description>Compute useful variant statistics</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -45,16 +45,30 @@
         <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">
             <expand macro="sanitize_query" />
         </param>
-
     </inputs>
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <!-- test vars-by-sample report -->
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
             <param name="stats_type" value="--vars-by-sample" />
-            <output name="outfile" file="gemini_stats_result.tabular" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="sample&#009;total" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- test gts-by-sample report -->
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
+            <param name="stats_type" value="--gts-by-sample" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="sample&#009;num_hom_ref&#009;num_het&#009;num_hom_alt&#009;num_unknown&#009;total" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff -r ee894347fcd6 -r cdd90678004a repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Oct 17 13:33:53 2018 -0400
+++ b/repository_dependencies.xml	Fri Dec 14 12:47:19 2018 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="172815da3d41" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="fe5a9a7d95b0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file
diff -r ee894347fcd6 -r cdd90678004a test-data/anno.bed
--- a/test-data/anno.bed	Wed Oct 17 13:33:53 2018 -0400
+++ b/test-data/anno.bed	Fri Dec 14 12:47:19 2018 -0500
@@ -1,3 +1,3 @@
-chr1	30547	30548
-chr1	30920	30925
-chr1	30922	30923
+chr3	187000000	187150000
+chr3	187150000	187300000
+chr3	187300000	187450000
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_amend.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_amend.ped	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,10 @@
+#family_id	sample_id	paternal_id	maternal_id	sex	phenotype
+1	1_dad	0	0	-1	1
+1	1_mom	0	0	-1	1
+1	1_kid	1_dad	1_mom	-1	2
+2	2_dad	0	0	-1	1
+2	2_mom	0	0	-1	1
+2	2_kid	2_dad	2_mom	-1	2
+3	3_dad	0	0	-1	1
+3	3_mom	0	0	-1	1
+3	3_kid	3_dad	3_mom	-1	2
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_amend.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_amend.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,127 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr10,length=135534747,assembly=hg19>
+##contig=<ID=chr11,length=135006516,assembly=hg19>
+##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
+##contig=<ID=chr12,length=133851895,assembly=hg19>
+##contig=<ID=chr13,length=115169878,assembly=hg19>
+##contig=<ID=chr14,length=107349540,assembly=hg19>
+##contig=<ID=chr15,length=102531392,assembly=hg19>
+##contig=<ID=chr16,length=90354753,assembly=hg19>
+##contig=<ID=chr17,length=81195210,assembly=hg19>
+##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
+##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
+##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
+##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
+##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
+##contig=<ID=chr18,length=78077248,assembly=hg19>
+##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
+##contig=<ID=chr19,length=59128983,assembly=hg19>
+##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
+##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
+##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
+##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr20,length=63025520,assembly=hg19>
+##contig=<ID=chr21,length=48129895,assembly=hg19>
+##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
+##contig=<ID=chr22,length=51304566,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
+##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
+##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
+##contig=<ID=chr5,length=180915260,assembly=hg19>
+##contig=<ID=chr6,length=171115067,assembly=hg19>
+##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
+##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
+##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
+##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
+##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
+##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
+##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
+##contig=<ID=chr7,length=159138663,assembly=hg19>
+##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
+##contig=<ID=chr8,length=146364022,assembly=hg19>
+##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
+##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
+##contig=<ID=chr9,length=141213431,assembly=hg19>
+##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
+##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
+##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
+##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
+##contig=<ID=chrM,length=16571,assembly=hg19>
+##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
+##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
+##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
+##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
+##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
+##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
+##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
+##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
+##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
+##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
+##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
+##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
+##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
+##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
+##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
+##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
+##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
+##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
+##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
+##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
+##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
+##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
+##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
+##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
+##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
+##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
+##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
+##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
+##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
+##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
+##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
+##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
+##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
+##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
+##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
+##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
+##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
+##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
+##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
+##contig=<ID=chrX,length=155270560,assembly=hg19>
+##contig=<ID=chrY,length=59373566,assembly=hg19>
+##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT">
+##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 test4.vep.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1_dad	1_mom	1_kid	2_dad	2_mom	2_kid	3_dad	3_mom	3_kid
+chr10	1142208	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:59:87.16:940,87,0	0/1:0,29:49:78.20:899,78,0	1/1:0,24:64:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	48003992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	48004992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135336656	.	G	A	38.34	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135369532	.	T	C	122.62	.	AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;DP=239;Dels=0.00;FS=5.194;HRun=2;HaplotypeScore=5.7141;MQ=36.02;MQ0=0;MQRankSum=0.082;QD=2.31;ReadPosRankSum=-0.695;CSQ=missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000303903|9/13|benign(0.001)|tolerated(1),missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000432597|10/14|benign(0)|tolerated(1),downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000460441|||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000343131|9/13|benign(0.001)|tolerated(1),intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000171772|SYCE1|ENST00000479535|6/10||,downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000482127|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000130649|CYP2E1|ENST00000368520|6/6||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000368517|9/13|benign(0)|tolerated(1);EFF=DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000460441|),DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000482127|),EXON(MODIFIER|||||CYP2E1|retained_intron|CODING|ENST00000368520|),EXON(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000479535|),INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000368517|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000432597|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|318|SYCE1|protein_coding|CODING|ENST00000303903|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|ENST00000343131|exon_10_135369485_135369551)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0
\ No newline at end of file
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_amend_input.db
Binary file test-data/gemini_amend_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_amend_input.ped
--- a/test-data/gemini_amend_input.ped	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#family_id name paternal_id maternal_id sex phenotype ethnicity hair_color
-1 M10475    None None  1    1    None	brown
-1 M10478     M10475  M10500    2    2    None	red
-1 M10500     None    None    2    2    None	
-1 M128215    M10475  M10500    1    1    None	green
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_amend_result.db
Binary file test-data/gemini_amend_result.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_annotate_input.db
Binary file test-data/gemini_annotate_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_annotate_result.db
Binary file test-data/gemini_annotate_result.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_annotate_result.tabular
--- a/test-data/gemini_annotate_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-updated 10 variants
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_auto_dom_input.db
Binary file test-data/gemini_auto_dom_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_auto_rec_input.db
Binary file test-data/gemini_auto_rec_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_autosomal_dominant_result.tabular
--- a/test-data/gemini_autosomal_dominant_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-gene	chrom	impact	variant_id	family_id	family_members	family_genotypes	samples	family_count
-ASAH2C	chr10	missense_variant	3	3	3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected)	C/T,C/C,C/T	3_dad,3_kid	2
-ASAH2C	chr10	missense_variant	3	2	2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected)	C/C,C/T,C/T	2_mom,2_kid	2
-ASAH2C	chr10	missense_variant	4	3	3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected)	C/T,C/C,C/T	3_dad,3_kid	2
-ASAH2C	chr10	missense_variant	4	2	2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected)	C/C,C/T,C/T	2_mom,2_kid	2
-SPRN	chr10	intron_variant	5	3	3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected)	G/A,G/G,G/A	3_dad,3_kid	1
-WDR37	chr10	stop_lost	1	3	3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected)	T/C,T/T,T/C	3_dad,3_kid	2
-WDR37	chr10	stop_lost	1	2	2_dad(2_dad;unaffected),2_mom(2_mom;affected),2_kid(2_kid;affected)	T/T,T/C,T/C	2_mom,2_kid	2
-WDR37	chr10	stop_lost	2	3	3_dad(3_dad;affected),3_mom(3_mom;unknown),3_kid(3_kid;affected)	T/C,T/C,T/C	3_dad,3_kid	2
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_autosomal_input.db
Binary file test-data/gemini_autosomal_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_autosomal_recessive.tabular
--- a/test-data/gemini_autosomal_recessive.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-gene	chrom	impact	variant_id	family_id	family_members	family_genotypes	samples	family_count
-WDR37	chr10	stop_lost	2	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/C,T/C,C/C	1_kid	1
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_burden_calpha_template.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_calpha_template.tabular	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,4 @@
+gene	T	c	Z	p_value
+SYCE1	.+	.+	.+	.+
+WDR37	.+	.+	.+	.+
+ASAH2C	.+	.+	.+	.+
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_burden_count_highimpact_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_count_highimpact_result.tabular	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,2 @@
+gene	1_kid	3_kid
+WDR37	1	2
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_burden_count_nonsynonymous_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_burden_count_nonsynonymous_result.tabular	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,5 @@
+gene	1_dad	1_kid	1_mom	2_dad	2_kid	2_mom	3_dad	3_kid	3_mom
+SYCE1	0	1	0	0	1	0	0	1	0
+SPRN	0	1	0	0	1	0	1	1	1
+WDR37	0	1	0	0	0	0	0	2	0
+ASAH2C	2	3	2	1	3	1	1	2	1
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_burden_input.db
Binary file test-data/gemini_burden_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_burden_result.tabular
--- a/test-data/gemini_burden_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-gene	T	c	Z	p_value
-SYCE1	-0.5	0.25	-1.0	0.00699300699301
-DHODH	0.0	0.0	nan	nan
-WDR37	-1.0	1.5	-0.816496580928	0.00699300699301
-ASAH2C	-0.5	0.75	-0.57735026919	0.00699300699301
-CTBP2	0.0	0.0	nan	nan
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_comphets_input.db
Binary file test-data/gemini_comphets_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_comphets_result.tabular
--- a/test-data/gemini_comphets_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-chrom	start	end	ref	alt	gene	impact	variant_id	family_id	family_members	family_genotypes	samples	family_count	comp_het_id	priority
-chr1	17362	17366	TTCT	T	WASH7P	splice_acceptor_variant	3	4	child_4(child_4;affected;male),dad_4(dad_4;unaffected;male),mom_4(mom_4;unaffected;female)	TTCT|T,TTCT/T,TTCT/TTCT	child_4	1	1_3_7	3
-chr1	17729	17730	C	A	WASH7P	splice_acceptor_variant	7	4	child_4(child_4;affected;male),dad_4(dad_4;unaffected;male),mom_4(mom_4;unaffected;female)	C/A,C/A,C/A	child_4	1	1_3_7	3
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_dbinfo_result.tabular
--- a/test-data/gemini_dbinfo_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,209 +0,0 @@
-table_name	column_name	type	
-variants	chrom	text	
-variants	start	integer	
-variants	end	integer	
-variants	vcf_id	text	
-variants	variant_id	integer	
-variants	anno_id	integer	
-variants	ref	text	
-variants	alt	text	
-variants	qual	float	
-variants	filter	text	
-variants	type	text	
-variants	sub_type	text	
-variants	gts	blob	
-variants	gt_types	blob	
-variants	gt_phases	blob	
-variants	gt_depths	blob	
-variants	gt_ref_depths	blob	
-variants	gt_alt_depths	blob	
-variants	gt_quals	blob	
-variants	gt_copy_numbers	blob	
-variants	gt_phred_ll_homref	blob	
-variants	gt_phred_ll_het	blob	
-variants	gt_phred_ll_homalt	blob	
-variants	call_rate	float	
-variants	in_dbsnp	bool	
-variants	rs_ids	text	
-variants	sv_cipos_start_left	integer	
-variants	sv_cipos_end_left	integer	
-variants	sv_cipos_start_right	integer	
-variants	sv_cipos_end_right	integer	
-variants	sv_length	integer	
-variants	sv_is_precise	bool	
-variants	sv_tool	text	
-variants	sv_evidence_type	text	
-variants	sv_event_id	text	
-variants	sv_mate_id	text	
-variants	sv_strand	text	
-variants	in_omim	bool	
-variants	clinvar_sig	text	
-variants	clinvar_disease_name	text	
-variants	clinvar_dbsource	text	
-variants	clinvar_dbsource_id	text	
-variants	clinvar_origin	text	
-variants	clinvar_dsdb	text	
-variants	clinvar_dsdbid	text	
-variants	clinvar_disease_acc	text	
-variants	clinvar_in_locus_spec_db	bool	
-variants	clinvar_on_diag_assay	bool	
-variants	clinvar_causal_allele	text	
-variants	pfam_domain	text	
-variants	cyto_band	text	
-variants	rmsk	text	
-variants	in_cpg_island	bool	
-variants	in_segdup	bool	
-variants	is_conserved	bool	
-variants	gerp_bp_score	float	
-variants	gerp_element_pval	float	
-variants	num_hom_ref	integer	
-variants	num_het	integer	
-variants	num_hom_alt	integer	
-variants	num_unknown	integer	
-variants	aaf	real	
-variants	hwe	decimal(2,7)
-variants	inbreeding_coeff	decimal(2,7)
-variants	pi	decimal(2,7)
-variants	recomb_rate	decimal(2,7)
-variants	gene	text	
-variants	transcript	text	
-variants	is_exonic	bool	
-variants	is_coding	bool	
-variants	is_splicing	bool	
-variants	is_lof	bool	
-variants	exon	text	
-variants	codon_change	text	
-variants	aa_change	text	
-variants	aa_length	text	
-variants	biotype	text	
-variants	impact	text	
-variants	impact_so	text	
-variants	impact_severity	text	
-variants	polyphen_pred	text	
-variants	polyphen_score	float	
-variants	sift_pred	text	
-variants	sift_score	float	
-variants	anc_allele	text	
-variants	rms_bq	float	
-variants	cigar	text	
-variants	depth	integer	
-variants	strand_bias	float	
-variants	rms_map_qual	float	
-variants	in_hom_run	integer	
-variants	num_mapq_zero	integer	
-variants	num_alleles	integer	
-variants	num_reads_w_dels	float	
-variants	haplotype_score	float	
-variants	qual_depth	float	
-variants	allele_count	integer	
-variants	allele_bal	float	
-variants	in_hm2	bool	
-variants	in_hm3	bool	
-variants	is_somatic	bool	
-variants	somatic_score	float	
-variants	in_esp	bool	
-variants	aaf_esp_ea	decimal(2,7)
-variants	aaf_esp_aa	decimal(2,7)
-variants	aaf_esp_all	decimal(2,7)
-variants	exome_chip	bool	
-variants	in_1kg	bool	
-variants	aaf_1kg_amr	decimal(2,7)
-variants	aaf_1kg_eas	decimal(2,7)
-variants	aaf_1kg_sas	decimal(2,7)
-variants	aaf_1kg_afr	decimal(2,7)
-variants	aaf_1kg_eur	decimal(2,7)
-variants	aaf_1kg_all	decimal(2,7)
-variants	grc	text	
-variants	gms_illumina	float	
-variants	gms_solid	float	
-variants	gms_iontorrent	float	
-variants	in_cse	bool	
-variants	encode_tfbs	text	
-variants	encode_dnaseI_cell_count	integer	
-variants	encode_dnaseI_cell_list	text	
-variants	encode_consensus_gm12878	text	
-variants	encode_consensus_h1hesc	text	
-variants	encode_consensus_helas3	text	
-variants	encode_consensus_hepg2	text	
-variants	encode_consensus_huvec	text	
-variants	encode_consensus_k562	text	
-variants	vista_enhancers	text	
-variants	cosmic_ids	text	
-variants	info	blob	
-variants	cadd_raw	float	
-variants	cadd_scaled	float	
-variants	fitcons	float	
-variants	in_exac	bool	
-variants	aaf_exac_all	decimal(2,7)
-variants	aaf_adj_exac_all	decimal(2,7)
-variants	aaf_adj_exac_afr	decimal(2,7)
-variants	aaf_adj_exac_amr	decimal(2,7)
-variants	aaf_adj_exac_eas	decimal(2,7)
-variants	aaf_adj_exac_fin	decimal(2,7)
-variants	aaf_adj_exac_nfe	decimal(2,7)
-variants	aaf_adj_exac_oth	decimal(2,7)
-variants	aaf_adj_exac_sas	decimal(2,7)
-variants	exac_num_het	int	
-variants	exac_num_hom_alt	int	
-variants	exac_num_chroms	int	
-variants	max_aaf_all	REAL	
-variant_impacts	variant_id	integer	
-variant_impacts	anno_id	integer	
-variant_impacts	gene	text	
-variant_impacts	transcript	text	
-variant_impacts	is_exonic	bool	
-variant_impacts	is_coding	bool	
-variant_impacts	is_splicing	bool	
-variant_impacts	is_lof	bool	
-variant_impacts	exon	text	
-variant_impacts	codon_change	text	
-variant_impacts	aa_change	text	
-variant_impacts	aa_length	text	
-variant_impacts	biotype	text	
-variant_impacts	impact	text	
-variant_impacts	impact_so	text	
-variant_impacts	impact_severity	text	
-variant_impacts	polyphen_pred	text	
-variant_impacts	polyphen_score	float	
-variant_impacts	sift_pred	text	
-variant_impacts	sift_score	float	
-samples	sample_id	integer	
-samples	family_id	text	
-samples	name	text	
-samples	paternal_id	text	
-samples	maternal_id	text	
-samples	sex	text	
-samples	phenotype	text	
-samples	ethnicity	text	
-gene_detailed	uid	integer	
-gene_detailed	chrom	text	
-gene_detailed	gene	text	
-gene_detailed	is_hgnc	bool	
-gene_detailed	ensembl_gene_id	text	
-gene_detailed	transcript	text	
-gene_detailed	biotype	text	
-gene_detailed	transcript_status	text	
-gene_detailed	ccds_id	text	
-gene_detailed	hgnc_id	text	
-gene_detailed	entrez_id	text	
-gene_detailed	cds_length	text	
-gene_detailed	protein_length	text	
-gene_detailed	transcript_start	text	
-gene_detailed	transcript_end	text	
-gene_detailed	strand	text	
-gene_detailed	synonym	text	
-gene_detailed	rvis_pct	float	
-gene_detailed	mam_phenotype_id	text	
-gene_summary	uid	integer	
-gene_summary	chrom	text	
-gene_summary	gene	text	
-gene_summary	is_hgnc	bool	
-gene_summary	ensembl_gene_id	text	
-gene_summary	hgnc_id	text	
-gene_summary	transcript_min_start	text	
-gene_summary	transcript_max_end	text	
-gene_summary	strand	text	
-gene_summary	synonym	text	
-gene_summary	rvis_pct	float	
-gene_summary	mam_phenotype_id	text	
-gene_summary	in_cosmic_census	bool	
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_de_novo_input.db
Binary file test-data/gemini_de_novo_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_de_novo_result.tabular
--- a/test-data/gemini_de_novo_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-chrom	start	end	vcf_id	variant_id	anno_id	ref	alt	qual	filter	type	sub_type	call_rate	in_dbsnp	rs_ids	sv_cipos_start_left	sv_cipos_end_left	sv_cipos_start_right	sv_cipos_end_right	sv_length	sv_is_precise	sv_tool	sv_evidence_type	sv_event_id	sv_mate_id	sv_strand	in_omim	clinvar_sig	clinvar_disease_name	clinvar_dbsource	clinvar_dbsource_id	clinvar_origin	clinvar_dsdb	clinvar_dsdbid	clinvar_disease_acc	clinvar_in_locus_spec_db	clinvar_on_diag_assay	clinvar_causal_allele	pfam_domain	cyto_band	rmsk	in_cpg_island	in_segdup	is_conserved	gerp_bp_score	gerp_element_pval	num_hom_ref	num_het	num_hom_alt	num_unknown	aaf	hwe	inbreeding_coeff	pi	recomb_rate	gene	transcript	is_exonic	is_coding	is_splicing	is_lof	exon	codon_change	aa_change	aa_length	biotype	impact	impact_so	impact_severity	polyphen_pred	polyphen_score	sift_pred	sift_score	anc_allele	rms_bq	cigar	depth	strand_bias	rms_map_qual	in_hom_run	num_mapq_zero	num_alleles	num_reads_w_dels	haplotype_score	qual_depth	allele_count	allele_bal	in_hm2	in_hm3	is_somatic	somatic_score	in_esp	aaf_esp_ea	aaf_esp_aa	aaf_esp_all	exome_chip	in_1kg	aaf_1kg_amr	aaf_1kg_eas	aaf_1kg_sas	aaf_1kg_afr	aaf_1kg_eur	aaf_1kg_all	grc	gms_illumina	gms_solid	gms_iontorrent	in_cse	encode_tfbs	encode_dnaseI_cell_count	encode_dnaseI_cell_list	encode_consensus_gm12878	encode_consensus_h1hesc	encode_consensus_helas3	encode_consensus_hepg2	encode_consensus_huvec	encode_consensus_k562	vista_enhancers	cosmic_ids	info	cadd_raw	cadd_scaled	fitcons	in_exac	aaf_exac_all	aaf_adj_exac_all	aaf_adj_exac_afr	aaf_adj_exac_amr	aaf_adj_exac_eas	aaf_adj_exac_fin	aaf_adj_exac_nfe	aaf_adj_exac_oth	aaf_adj_exac_sas	exac_num_het	exac_num_hom_alt	exac_num_chroms	max_aaf_all	gts	gt_types	gt_phases	gt_depths	gt_ref_depths	gt_alt_depths	gt_quals	gt_copy_numbers	gt_phred_ll_homref	gt_phred_ll_het	gt_phred_ll_homalt	family_id	family_members	family_genotypes	samples	family_count
-chr10	48003991	48003992	None	2	1	C	T	1047.86999512	None	snp	ts	1.0	1	rs142685947,rs3739968	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	1	None	3.10871e-42	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	1	0.3112	0.4573	0.3855	0.1241	0.5149	0.346645	grc_fix	73.3	40.3	92.8	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.553676	1	0.443	0.448537771896	0.288974151858	0.281426746944	0.543088975937	0.524984286612	0.478147713207	0.463529411765	0.418641164716	17495	15317	107302	0.543088975937	['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T']	[1 1 3 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	C/C,C/C,C/T	2_kid	2
-chr10	48004991	48004992	None	3	1	C	T	1047.86999512	None	snp	ts	1.0	0	None	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	0	None	None	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	0	None	None	None	None	None	None	grc_fix	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.061011	0	None	None	None	None	None	None	None	None	None	None	None	None	-1.0	['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T']	[1 1 1 1 1 3 0 0 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	C/C,C/C,C/T	3_kid	2
-chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	G/G,G/G,G/A	1_kid	2
-chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	G/G,G/G,G/A	2_kid	2
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	3
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,T/C	3_kid	3
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	T/T,T/T,T/C	2_kid	3
-chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	1
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_dump_result.tabular
--- a/test-data/gemini_dump_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-chrom	start	end	ref	alt	type	sub_type	aaf	in_dbsnp	gene	sample	genotype
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_1	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_2	G/G
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_2	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_2	G/G
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_1	G/G
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_1	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_3	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_3	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_3	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_4	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_4	G/A
-chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_4	G/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_1	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_2	A/G
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_2	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_2	A/G
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_1	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_1	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_3	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_3	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_3	A/G
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_4	A/G
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_4	A/A
-chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_4	A/A
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_1	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_2	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_2	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_2	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_1	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_1	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_3	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_3	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_3	TTCT/TTCT
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_4	TTCT/T
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_4	TTCT/T
-chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_4	TTCT/TTCT
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_1	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_2	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_2	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_2	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_1	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_1	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_3	G/A
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_3	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_3	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_4	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_4	G/G
-chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_4	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_1	G/C
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_2	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_2	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_2	G/C
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_1	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_1	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_3	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_3	G/C
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_3	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_4	G/C
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_4	G/G
-chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_4	G/G
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_1	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_2	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_2	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_2	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_1	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_1	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_3	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_3	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_3	A/A
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_4	A/G
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_4	A/G
-chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_4	A/G
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_1	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_2	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_2	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_2	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_1	C/A
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_1	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_3	C/A
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_3	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_3	C/C
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_4	C/A
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_4	C/A
-chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_4	C/A
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_1	A/A
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_2	A/A
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_2	A/A
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_2	A/A
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_1	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_1	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_3	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_3	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_3	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_4	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_4	A/G
-chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_4	A/G
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_gene_wise_result.tabular
--- a/test-data/gemini_gene_wise_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-chrom	start	end	gene	impact	impact_severity	max_aaf_all	variant_filters	n_gene_variants	gene_filters
-chr10	48003991	48003992	ASAH2C	missense_variant	MED	0.543088975937	1	1	1
-chr10	126678091	126678092	CTBP2	stop_gained	HIGH	0.0904917363803	1	1	1
-chr10	135369531	135369532	SYCE1	missense_variant	MED	0.2698	1	1	1
-chr10	1142207	1142208	WDR37	stop_lost	HIGH	1.0	1	1	1
-chr16	72057434	72057435	DHODH	missense_variant	MED	0.000432002764818	1	1	1
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_interactions_result.tabular
--- a/test-data/gemini_interactions_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-sample	gene	order_of_interaction	interacting_gene
-M10475	CTBP2	0_order:	none
-M10475	CTBP2	1_order:	none
-M10475	CTBP2	2_order:	none
-M10475	CTBP2	3_order:	none
-M10475	CTBP2	4_order:	WDR37
-M10475	CTBP2	5_order:	none
-M128215	CTBP2	0_order:	CTBP2
-M128215	CTBP2	1_order:	none
-M128215	CTBP2	2_order:	none
-M128215	CTBP2	3_order:	none
-M128215	CTBP2	4_order:	WDR37
-M128215	CTBP2	5_order:	none
-M10478	CTBP2	0_order:	none
-M10478	CTBP2	1_order:	none
-M10478	CTBP2	2_order:	none
-M10478	CTBP2	3_order:	none
-M10478	CTBP2	4_order:	WDR37
-M10478	CTBP2	5_order:	MTG1
-M10500	CTBP2	0_order:	none
-M10500	CTBP2	1_order:	none
-M10500	CTBP2	2_order:	none
-M10500	CTBP2	3_order:	none
-M10500	CTBP2	4_order:	WDR37
-M10500	CTBP2	5_order:	MTG1
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_is_somatic_result.db
Binary file test-data/gemini_is_somatic_result.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_load_result.db
Binary file test-data/gemini_load_result.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_load_result1.db
Binary file test-data/gemini_load_result1.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_load_result2.db
Binary file test-data/gemini_load_result2.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_lofsieve_result.tabular
--- a/test-data/gemini_lofsieve_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-chrom	start	end	ref	alt	highest_impact	aa_change	var_trans_pos	trans_aa_length	var_trans_pct	sample	genotype	gene	transcript	trans_type
-chr10	1142207	1142208	T	C	stop_lost	*/R	250	250/249	1.00401606426	M10475	C/C	WDR37	ENST00000381329	protein_coding
-chr10	1142207	1142208	T	C	stop_lost	*/R	250	250/249	1.00401606426	M10478	C/C	WDR37	ENST00000381329	protein_coding
-chr10	1142207	1142208	T	C	stop_lost	*/R	250	250/249	1.00401606426	M10500	C/C	WDR37	ENST00000381329	protein_coding
-chr10	1142207	1142208	T	C	stop_lost	*/R	250	250/249	1.00401606426	M128215	C/C	WDR37	ENST00000381329	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000531469	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000309035	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000494626	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000337195	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000334808	protein_coding
-chr10	126678091	126678092	G	A	stop_gained	Q/*	445	445/445	1.0	M128215	G/A	CTBP2	ENST00000411419	protein_coding
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_mendel_errors_result.tabular
--- a/test-data/gemini_mendel_errors_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-chrom	start	end	vcf_id	variant_id	anno_id	ref	alt	qual	filter	type	sub_type	call_rate	in_dbsnp	rs_ids	sv_cipos_start_left	sv_cipos_end_left	sv_cipos_start_right	sv_cipos_end_right	sv_length	sv_is_precise	sv_tool	sv_evidence_type	sv_event_id	sv_mate_id	sv_strand	in_omim	clinvar_sig	clinvar_disease_name	clinvar_dbsource	clinvar_dbsource_id	clinvar_origin	clinvar_dsdb	clinvar_dsdbid	clinvar_disease_acc	clinvar_in_locus_spec_db	clinvar_on_diag_assay	clinvar_causal_allele	pfam_domain	cyto_band	rmsk	in_cpg_island	in_segdup	is_conserved	gerp_bp_score	gerp_element_pval	num_hom_ref	num_het	num_hom_alt	num_unknown	aaf	hwe	inbreeding_coeff	pi	recomb_rate	gene	transcript	is_exonic	is_coding	is_splicing	is_lof	exon	codon_change	aa_change	aa_length	biotype	impact	impact_so	impact_severity	polyphen_pred	polyphen_score	sift_pred	sift_score	anc_allele	rms_bq	cigar	depth	strand_bias	rms_map_qual	in_hom_run	num_mapq_zero	num_alleles	num_reads_w_dels	haplotype_score	qual_depth	allele_count	allele_bal	in_hm2	in_hm3	is_somatic	somatic_score	in_esp	aaf_esp_ea	aaf_esp_aa	aaf_esp_all	exome_chip	in_1kg	aaf_1kg_amr	aaf_1kg_eas	aaf_1kg_sas	aaf_1kg_afr	aaf_1kg_eur	aaf_1kg_all	grc	gms_illumina	gms_solid	gms_iontorrent	in_cse	encode_tfbs	encode_dnaseI_cell_count	encode_dnaseI_cell_list	encode_consensus_gm12878	encode_consensus_h1hesc	encode_consensus_helas3	encode_consensus_hepg2	encode_consensus_huvec	encode_consensus_k562	vista_enhancers	cosmic_ids	info	cadd_raw	cadd_scaled	fitcons	in_exac	aaf_exac_all	aaf_adj_exac_all	aaf_adj_exac_afr	aaf_adj_exac_amr	aaf_adj_exac_eas	aaf_adj_exac_fin	aaf_adj_exac_nfe	aaf_adj_exac_oth	aaf_adj_exac_sas	exac_num_het	exac_num_hom_alt	exac_num_chroms	max_aaf_all	gts	gt_types	gt_phases	gt_depths	gt_ref_depths	gt_alt_depths	gt_quals	gt_copy_numbers	gt_phred_ll_homref	gt_phred_ll_het	gt_phred_ll_homalt	family_id	family_members	family_genotypes	samples	family_count	violation	violation_prob
-chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	2	plausible de novo;implausible de novo	0.00000
-chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,C/C	3_kid	2	plausible de novo;implausible de novo	0.00000
-chr10	48003991	48003992	None	2	1	C	T	1047.86999512	None	snp	ts	1.0	1	rs142685947,rs3739968	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	1	None	3.10871e-42	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	1	0.3112	0.4573	0.3855	0.1241	0.5149	0.346645	grc_fix	73.3	40.3	92.8	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.553676	1	0.443	0.448537771896	0.288974151858	0.281426746944	0.543088975937	0.524984286612	0.478147713207	0.463529411765	0.418641164716	17495	15317	107302	0.543088975937	['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T']	[1 1 3 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	C/C,C/C,C/T	2_kid	1	plausible de novo	0.00000
-chr10	48004991	48004992	None	3	1	C	T	1047.86999512	None	snp	ts	1.0	0	None	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	0	None	None	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	0	None	None	None	None	None	None	grc_fix	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.061011	0	None	None	None	None	None	None	None	None	None	None	None	None	-1.0	['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T']	[1 1 1 1 1 3 0 0 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	C/C,C/C,C/T	3_kid	1	plausible de novo	0.00000
-chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	G/G,G/G,G/A	1_kid	2	plausible de novo;plausible de novo	0.00000
-chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	G/G,G/G,G/A	2_kid	2	plausible de novo;plausible de novo	0.00000
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,T/C	3_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
-chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	T/T,T/T,T/C	2_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_pathways_result.tabular
--- a/test-data/gemini_pathways_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-chrom	start	end	ref	alt	impact	sample	genotype	gene	transcript	pathway
-chr10	52004314	52004315	T	C	intron_variant	M10500	C/C	ASAH2	ENST00000329428	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	52004314	52004315	T	C	intron_variant	M128215	C/C	ASAH2	ENST00000329428	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	52004314	52004315	T	C	intron_variant	M10500	C/C	ASAH2	ENST00000447815	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	52004314	52004315	T	C	intron_variant	M128215	C/C	ASAH2	ENST00000447815	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	52004314	52004315	T	C	intron_variant	M10500	C/C	ASAH2	ENST00000395526	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	52004314	52004315	T	C	intron_variant	M128215	C/C	ASAH2	ENST00000395526	hsa00600:Sphingolipid_metabolism,hsa01100:Metabolic_pathways
-chr10	126678091	126678092	G	A	stop_gained	M128215	G/A	CTBP2	ENST00000531469	hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer
-chr10	126678091	126678092	G	A	stop_gained	M128215	G/A	CTBP2	ENST00000309035	hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer
-chr10	126678091	126678092	G	A	stop_gained	M128215	G/A	CTBP2	ENST00000494626	hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer
-chr10	126678091	126678092	G	A	stop_gained	M128215	G/A	CTBP2	ENST00000337195	hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer
-chr10	126678091	126678092	G	A	stop_gained	M128215	G/A	CTBP2	ENST00000411419	hsa05220:Chronic_myeloid_leukemia,hsa04310:Wnt_signaling_pathway,hsa04330:Notch_signaling_pathway,hsa05200:Pathways_in_cancer
-chr10	135336655	135336656	G	A	intron_variant	M10478	A/A	CYP2E1	ENST00000463117	hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism
-chr10	135336655	135336656	G	A	intron_variant	M128215	A/A	CYP2E1	ENST00000463117	hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism
-chr10	135336655	135336656	G	A	upstream_gene_variant	M10478	A/A	CYP2E1	ENST00000252945	hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism
-chr10	135336655	135336656	G	A	upstream_gene_variant	M128215	A/A	CYP2E1	ENST00000252945	hsa00982:Drug_metabolism_cytochrome_P450,hsa01100:Metabolic_pathways,hsa00590:Arachidonic_acid_metabolism,hsa00980:Metabolism_of_xenobiotics_by_cytochrome_P450,hsa00591:Linoleic_acid_metabolism
-chr16	72057434	72057435	C	T	missense_variant	M10475	C/T	DHODH	ENST00000219240	hsa01100:Metabolic_pathways,hsa00240:Pyrimidine_metabolism
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_qc_result.tabular
--- a/test-data/gemini_qc_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-sample	sex	chrX_homref	chrX_het	chrX_homalt	chrX_unknown
-M10475	male	0	0	0	0
-M10478	female	0	0	0	0
-M10500	female	0	0	0	0
-M128215	male	0	0	0	0
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_query_result.tabular
--- a/test-data/gemini_query_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-10582
-10610
-13301
-13326
-13956
-13979
-30922
-46401
-47189
-51475
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_region_result.tabular
--- a/test-data/gemini_region_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-chr10	48003991	48003992	None	2	1	C	T	1047.86999512	None	snp	ts	1.0	1	rs142685947,rs3739968	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	1	None	3.10871e-42	1	2	1	0	0.5	1	0	0.571428571429	1.718591	ASAH2C	ENST00000420079	1	1	0	0	16/17	tGt/tAt	C/Y	542/612	protein_coding	missense_variant	missense_variant	MED	benign	0.0	tolerated	1.0	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	1	0.3112	0.4573	0.3855	0.1241	0.5149	0.346645	grc_fix	73.3	40.3	92.8	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.553676	1	0.443	0.448537771896	0.288974151858	0.281426746944	0.543088975937	0.524984286612	0.478147713207	0.463529411765	0.418641164716	17495	15317	107302	1	0.543088975937
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_roh_result.tabular
--- a/test-data/gemini_roh_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-chrom	start	end	sample	num_of_snps	density_per_kb	run_length_in_bp
-chr10	1142208	135369532	M10475	5	0.0	134227324
-chr10	1142208	135210791	M10500	5	0.0001	134068583
-chr10	1142208	135210791	M10478	5	0.0001	134068583
-chr10	1142208	135336656	M10478	4	0.0	134194448
-chr10	1142208	135336656	M128215	6	0.0001	134194448
-chr10	1142208	135369532	M128215	5	0.0	134227324
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_stats_result.tabular
--- a/test-data/gemini_stats_result.tabular	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-sample	total
-M10475	3
-M10478	6
-M10500	6
-M128215	4
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_versioned_databases.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_versioned_databases.loc	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,3 @@
+## GEMINI versioned databases
+#DownloadDate	dbkey	DBversion	Description	Path
+1999-01-01	hg19	181	GEMINI annotations (test snapshot)	${__HERE__}/test-cache
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_windower_input.db
Binary file test-data/gemini_windower_input.db has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/gemini_windower_template.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_windower_template.tabular	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,142 @@
+chr1	0	50000	.
+chr1	50000000	50050000	.
+chr1	100000000	100050000	.
+chr1	150000000	150050000	.
+chr1	200000000	200050000	.
+chr10	0	50000	.
+chr10	50000000	50050000	.
+chr10	100000000	100050000	.
+chr11	0	50000	.
+chr11	50000000	50050000	.
+chr11	100000000	100050000	.
+chr11_gl000202_random	0	40103	.
+chr12	0	50000	.
+chr12	50000000	50050000	.
+chr12	100000000	100050000	.
+chr13	0	50000	.
+chr13	50000000	50050000	.
+chr13	100000000	100050000	.
+chr14	0	50000	.
+chr14	50000000	50050000	.
+chr14	100000000	100050000	.
+chr15	0	50000	.
+chr15	50000000	50050000	.
+chr15	100000000	100050000	.
+chr16	0	50000	.
+chr16	50000000	50050000	.
+chr17	0	50000	.
+chr17	50000000	50050000	.
+chr17_ctg5_hap1	0	50000	.
+chr17_gl000203_random	0	37498	.
+chr17_gl000204_random	0	50000	.
+chr17_gl000205_random	0	50000	.
+chr17_gl000206_random	0	41001	.
+chr18	0	50000	.
+chr18	50000000	50050000	.
+chr18_gl000207_random	0	4262	.
+chr19	0	50000	.
+chr19	50000000	50050000	.
+chr19_gl000208_random	0	50000	.
+chr19_gl000209_random	0	50000	.
+chr1_gl000191_random	0	50000	.
+chr1_gl000192_random	0	50000	.
+chr2	0	50000	.
+chr2	50000000	50050000	.
+chr2	100000000	100050000	.
+chr2	150000000	150050000	.
+chr2	200000000	200050000	.
+chr20	0	50000	.
+chr20	50000000	50050000	.
+chr21	0	50000	.
+chr21_gl000210_random	0	27682	.
+chr22	0	50000	.
+chr22	50000000	50050000	.
+chr3	0	50000	.
+chr3	50000000	50050000	.
+chr3	100000000	100050000	.
+chr3	150000000	150050000	.
+chr4	0	50000	.
+chr4	50000000	50050000	.
+chr4	100000000	100050000	.
+chr4	150000000	150050000	.
+chr4_ctg9_hap1	0	50000	.
+chr4_gl000193_random	0	50000	.
+chr4_gl000194_random	0	50000	.
+chr5	0	50000	.
+chr5	50000000	50050000	.
+chr5	100000000	100050000	.
+chr5	150000000	150050000	.
+chr6	0	50000	.
+chr6	50000000	50050000	.
+chr6	100000000	100050000	.
+chr6	150000000	150050000	.
+chr6_apd_hap1	0	50000	.
+chr6_cox_hap2	0	50000	.
+chr6_dbb_hap3	0	50000	.
+chr6_mann_hap4	0	50000	.
+chr6_mcf_hap5	0	50000	.
+chr6_qbl_hap6	0	50000	.
+chr6_ssto_hap7	0	50000	.
+chr7	0	50000	.
+chr7	50000000	50050000	.
+chr7	100000000	100050000	.
+chr7	150000000	150050000	.
+chr7_gl000195_random	0	50000	.
+chr8	0	50000	.
+chr8	50000000	50050000	.
+chr8	100000000	100050000	.
+chr8_gl000196_random	0	38914	.
+chr8_gl000197_random	0	37175	.
+chr9	0	50000	.
+chr9	50000000	50050000	.
+chr9	100000000	100050000	.
+chr9_gl000198_random	0	50000	.
+chr9_gl000199_random	0	50000	.
+chr9_gl000200_random	0	50000	.
+chr9_gl000201_random	0	36148	.
+chrM	0	16571	.
+chrUn_gl000211	0	50000	.
+chrUn_gl000212	0	50000	.
+chrUn_gl000213	0	50000	.
+chrUn_gl000214	0	50000	.
+chrUn_gl000215	0	50000	.
+chrUn_gl000216	0	50000	.
+chrUn_gl000217	0	50000	.
+chrUn_gl000218	0	50000	.
+chrUn_gl000219	0	50000	.
+chrUn_gl000220	0	50000	.
+chrUn_gl000221	0	50000	.
+chrUn_gl000222	0	50000	.
+chrUn_gl000223	0	50000	.
+chrUn_gl000224	0	50000	.
+chrUn_gl000225	0	50000	.
+chrUn_gl000226	0	15008	.
+chrUn_gl000227	0	50000	.
+chrUn_gl000228	0	50000	.
+chrUn_gl000229	0	19913	.
+chrUn_gl000230	0	43691	.
+chrUn_gl000231	0	27386	.
+chrUn_gl000232	0	40652	.
+chrUn_gl000233	0	45941	.
+chrUn_gl000234	0	40531	.
+chrUn_gl000235	0	34474	.
+chrUn_gl000236	0	41934	.
+chrUn_gl000237	0	45867	.
+chrUn_gl000238	0	39939	.
+chrUn_gl000239	0	33824	.
+chrUn_gl000240	0	41933	.
+chrUn_gl000241	0	42152	.
+chrUn_gl000242	0	43523	.
+chrUn_gl000243	0	43341	.
+chrUn_gl000244	0	39929	.
+chrUn_gl000245	0	36651	.
+chrUn_gl000246	0	38154	.
+chrUn_gl000247	0	36422	.
+chrUn_gl000248	0	39786	.
+chrUn_gl000249	0	38502	.
+chrX	0	50000	.
+chrX	50000000	50050000	.
+chrX	100000000	100050000	.
+chrX	150000000	150050000	.
+chrY	0	50000	.
+chrY	50000000	50050000	.
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini-config.yaml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini-config.yaml	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,13 @@
+annotation_dir: gemini/data
+versions:
+  ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4
+  ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2
+  ExAC.r0.3.sites.vep.tidy.vcf.gz: 3
+  GRCh37-gms-mappability.vcf.gz: 2
+  clinvar_20160203.tidy.vcf.gz: 5
+  cosmic-v68-GRCh37.tidy.vcf.gz: 3
+  dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4
+  detailed_gene_table_v75: 2
+  geno2mp.variants.tidy.vcf.gz: 1
+  hg19.rmsk.bed.gz: 2
+  summary_gene_table_v75: 2
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/cancer_gene_census.20140120.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/cancer_gene_census.20140120.tsv	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,19 @@
+ARHH	"RAS homolog gene family, member H (TTF)"	399	4	4p13 	yes		NHL			L	Dom	T	BCL6							
+BCL5	B-cell CLL/lymphoma 5	603	17	17q22 	yes		CLL			L	Dom	T	MYC							
+BCL6	B-cell CLL/lymphoma 6	604	3	3q27 	yes		"NHL, CLL"			L	Dom	"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"							
+BCOR	BCL6 corepressor	54880	X	Xp11.4	yes		"retinoblastoma, AML, APL (translocation)"				Rec	"F, N, S, T"	RARA	yes	oculo-facio-cardio-dental genetic					
+CIITA	"class II, major histocompatibility complex, transactivator"	4261	16	16p13	yes		"PMBL, Hodgkin lymphoma"			L	Dom	T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"							
+EIF4A2	"eukaryotic translation initiation factor 4A, isoform 2"	1974	3	3q27.3	yes		NHL			L	Dom	T	BCL6							
+HIST1H4I	"histone 1, H4i (H4FM)"	8294	6	6p21.3 	yes		NHL			L	Dom	T	BCL6							
+HSPCA	"heat shock 90kDa protein 1, alpha"	3320	14	14q32.31	yes		NHL			L	Dom	T	BCL6							
+HSPCB	"heat shock 90kDa protein 1, beta"	3326	6	6p12	yes		NHL			L	Dom	T	BCL6							
+IGH@	immunoglobulin heavy locus	3492	14	14q32.33	yes		"MM, Burkitt lymphoma, NHL, CLL, B-ALL, MALT, MLCLS"			L	Dom	T	"MYC, FGFR3,PAX5, IRTA1, IRF4, CCND1, BCL9, BCL8, BCL6, BCL2, BCL3, BCL10, BCL11A. LHX4, DDX6, NFKB2, PAFAH1B2, PCSK7, CRLF2"							
+IKZF1	IKAROS family zinc finger 1	10320	7	7p12.2	yes		"ALL, DLBCL"			L	"Rec,Dom"	"D,T"	BCL6							
+IL21R	interleukin 21 receptor	50615	16	16p11 	yes		NHL			L	Dom	T	BCL6							
+LCP1	lymphocyte cytosolic protein 1 (L-plastin)	3936	13	 13q14.1-q14.3 	yes		NHL 			L	Dom	T	BCL6							
+MYC	v-myc myelocytomatosis viral oncogene homolog (avian)	4609	8	8q24.12-q24.13 	yes		"Burkitt lymphoma, amplified in other cancers, B-CLL"			"L, E"	Dom	"A, T"	"IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"							
+NACA	nascent-polypeptide-associated complex alpha polypeptide	4666	12	12q23-q24.1 	yes		NHL			L	Dom	T	BCL6							
+PIM1	pim-1 oncogene	5292	6	6p21.2 	yes		NHL			L	Dom	T	BCL6							
+POU2AF1	"POU domain, class 2, associating factor 1 (OBF1)"	5450	11	11q23.1 	yes		NHL			L	Dom	T	BCL6							
+SFRS3	"splicing factor, arginine/serine-rich 3"	6428	6	6p21	yes		follicular lymphoma			L	Dom	T	BCL6							
+TFRC	"transferrin receptor (p90, CD71)"	7037	3	3q29 	yes		NHL			L	Dom	T	BCL6							
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/detailed_gene_table_v75
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/detailed_gene_table_v75	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,114 @@
+Chromosome	Gene_name	Is_hgnc	Ensembl_gene_id	Ensembl_transcript_id	Biotype	Transcript_status	CCDS_id	HGNC_id	CDS_length	Protein_length	Transcript_start	Transcript_end	strand	Synonyms	Rvis_pct	entrez_gene_id	mammalian_phenotype_id
+chr3	None	0	ENSG00000239093	ENST00000459452	snoRNA	KNOWN	None	None	None	None	187141103	187141207	1	None	None	None	None
+chr3	None	0	ENSG00000228952	ENST00000440726	lincRNA	KNOWN	None	None	None	None	187166633	187167238	1	None	None	None	None
+chr3	None	0	ENSG00000223401	ENST00000450760	lincRNA	KNOWN	None	None	None	None	187461474	187463208	1	None	None	None	None
+chr3	MASP	0	ENSG00000127241	ENST00000337774	protein_coding	KNOWN	CCDS33907	None	2100	699	186935942	187009810	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000337774	protein_coding	KNOWN	CCDS33907	None	2100	699	186935942	187009810	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000337774	protein_coding	KNOWN	CCDS33907	6901	2100	699	186935942	187009810	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000337774	protein_coding	KNOWN	CCDS33907	None	2100	699	186935942	187009810	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000296280	protein_coding	KNOWN	CCDS33908	None	2187	728	186951870	187009646	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000296280	protein_coding	KNOWN	CCDS33908	None	2187	728	186951870	187009646	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000296280	protein_coding	KNOWN	CCDS33908	6901	2187	728	186951870	187009646	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000296280	protein_coding	KNOWN	CCDS33908	None	2187	728	186951870	187009646	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000392472	protein_coding	PUTATIVE	None	None	1848	615	186951872	187009765	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000392472	protein_coding	PUTATIVE	None	None	1848	615	186951872	187009765	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000392472	protein_coding	PUTATIVE	None	6901	1848	615	186951872	187009765	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000392472	protein_coding	PUTATIVE	None	None	1848	615	186951872	187009765	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000495249	processed_transcript	PUTATIVE	None	None	None	None	186953655	187009542	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000495249	processed_transcript	PUTATIVE	None	None	None	None	186953655	187009542	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000495249	processed_transcript	PUTATIVE	None	6901	None	None	186953655	187009542	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000495249	processed_transcript	PUTATIVE	None	None	None	None	186953655	187009542	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000169293	protein_coding	KNOWN	CCDS33909	None	1143	380	186964149	187009745	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000169293	protein_coding	KNOWN	CCDS33909	None	1143	380	186964149	187009745	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000169293	protein_coding	KNOWN	CCDS33909	6901	1143	380	186964149	187009745	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000169293	protein_coding	KNOWN	CCDS33909	None	1143	380	186964149	187009745	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000392470	protein_coding	PUTATIVE	None	None	1065	354	186964947	187009670	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000392470	protein_coding	PUTATIVE	None	None	1065	354	186964947	187009670	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000392470	protein_coding	PUTATIVE	None	6901	1065	354	186964947	187009670	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000392470	protein_coding	PUTATIVE	None	None	1065	354	186964947	187009670	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000460839	retained_intron	KNOWN	None	None	None	None	186974373	187003796	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000460839	retained_intron	KNOWN	None	None	None	None	186974373	187003796	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000460839	retained_intron	KNOWN	None	6901	None	None	186974373	187003796	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000460839	retained_intron	KNOWN	None	None	None	None	186974373	187003796	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000392475	protein_coding	NOVEL	None	None	614	203	186974603	187009768	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000392475	protein_coding	NOVEL	None	None	614	203	186974603	187009768	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000392475	protein_coding	NOVEL	None	6901	614	203	186974603	187009768	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000392475	protein_coding	NOVEL	None	None	614	203	186974603	187009768	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000439271	protein_coding	PUTATIVE	None	None	355	117	186980469	187009746	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000439271	protein_coding	PUTATIVE	None	None	355	117	186980469	187009746	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000439271	protein_coding	PUTATIVE	None	6901	355	117	186980469	187009746	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000439271	protein_coding	PUTATIVE	None	None	355	117	186980469	187009746	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	MASP	0	ENSG00000127241	ENST00000425937	protein_coding	PUTATIVE	None	None	166	54	186980502	187009485	-1	PRSS5,MASP1,CRARF	16.8141071	5648	None
+chr3	PRSS5	0	ENSG00000127241	ENST00000425937	protein_coding	PUTATIVE	None	None	166	54	186980502	187009485	-1	MASP1,CRARF,MASP	16.8141071	5648	None
+chr3	MASP1	1	ENSG00000127241	ENST00000425937	protein_coding	PUTATIVE	None	6901	166	54	186980502	187009485	-1	PRSS5,CRARF,MASP	16.8141071	5648	None
+chr3	CRARF	0	ENSG00000127241	ENST00000425937	protein_coding	PUTATIVE	None	None	166	54	186980502	187009485	-1	PRSS5,MASP1,MASP	16.8141071	5648	None
+chr3	IFRG28	0	ENSG00000136514	ENST00000259030	protein_coding	KNOWN	CCDS33910	None	741	246	187086120	187089864	1	RTP4,Z3CXXC4	94.35008257	64108	None
+chr3	RTP4	1	ENSG00000136514	ENST00000259030	protein_coding	KNOWN	CCDS33910	23992	741	246	187086120	187089864	1	IFRG28,Z3CXXC4	94.35008257	64108	None
+chr3	Z3CXXC4	0	ENSG00000136514	ENST00000259030	protein_coding	KNOWN	CCDS33910	None	741	246	187086120	187089864	1	IFRG28,RTP4	94.35008257	64108	None
+chr3	SST	1	ENSG00000157005	ENST00000287641	protein_coding	KNOWN	CCDS3288	11329	351	116	187386694	187388187	-1	SMST	78.16112291	6750	MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3	SMST	0	ENSG00000157005	ENST00000287641	protein_coding	KNOWN	CCDS3288	None	351	116	187386694	187388187	-1	SST	78.16112291	6750	MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3	Z3CXXC2	0	ENSG00000198471	ENST00000358241	protein_coding	KNOWN	CCDS33911	None	678	225	187416047	187420345	-1	RTP2,MGC78665	69.20853975	344892	MP:0005389
+chr3	RTP2	1	ENSG00000198471	ENST00000358241	protein_coding	KNOWN	CCDS33911	32486	678	225	187416047	187420345	-1	Z3CXXC2,MGC78665	69.20853975	344892	MP:0005389
+chr3	MGC78665	0	ENSG00000198471	ENST00000358241	protein_coding	KNOWN	CCDS33911	None	678	225	187416047	187420345	-1	Z3CXXC2,RTP2	69.20853975	344892	MP:0005389
+chr3	None	0	ENSG00000228804	ENST00000449623	protein_coding	PUTATIVE	None	None	390	129	187420101	187451637	1	None	None	None	None
+chr3	None	0	ENSG00000228804	ENST00000437407	protein_coding	PUTATIVE	None	None	153	50	187420154	187450203	1	None	None	None	None
+chr3	ZNF51	0	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	None	2121	706	187439165	187463515	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	None	2121	706	187439165	187463515	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	None	2121	706	187439165	187463515	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	None	2121	706	187439165	187463515	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	1001	2121	706	187439165	187463515	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000406870	protein_coding	KNOWN	CCDS3289	None	2121	706	187439165	187463515	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	None	168	55	187439175	187454876	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	None	168	55	187439175	187454876	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	None	168	55	187439175	187454876	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	None	168	55	187439175	187454876	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	1001	168	55	187439175	187454876	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000419510	nonsense_mediated_decay	KNOWN	None	None	168	55	187439175	187454876	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	None	2121	706	187440186	187454357	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	None	2121	706	187440186	187454357	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	None	2121	706	187440186	187454357	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	None	2121	706	187440186	187454357	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	1001	2121	706	187440186	187454357	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000232014	protein_coding	KNOWN	CCDS3289	None	2121	706	187440186	187454357	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	None	1953	650	187440220	187452670	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	None	1953	650	187440220	187452670	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	None	1953	650	187440220	187452670	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	None	1953	650	187440220	187452670	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	1001	1953	650	187440220	187452670	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000450123	protein_coding	NOVEL	CCDS46975	None	1953	650	187440220	187452670	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	None	None	None	187442357	187443411	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	None	None	None	187442357	187443411	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	None	None	None	187442357	187443411	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	None	None	None	187442357	187443411	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	1001	None	None	187442357	187443411	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000479110	retained_intron	KNOWN	None	None	None	None	187442357	187443411	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	None	365	120	187449515	187452735	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	None	365	120	187449515	187452735	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	None	365	120	187449515	187452735	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	None	365	120	187449515	187452735	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	1001	365	120	187449515	187452735	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000430339	protein_coding	KNOWN	None	None	365	120	187449515	187452735	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	None	None	None	187449553	187463225	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	None	None	None	187449553	187463225	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	None	None	None	187449553	187463225	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	None	None	None	187449553	187463225	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	1001	None	None	187449553	187463225	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000480458	processed_transcript	KNOWN	None	None	None	None	187449553	187463225	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	None	312	103	187449568	187455732	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	None	312	103	187449568	187455732	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	None	312	103	187449568	187455732	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	None	312	103	187449568	187455732	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	1001	312	103	187449568	187455732	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000438077	protein_coding	KNOWN	None	None	312	103	187449568	187455732	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	None	None	None	187452233	187463260	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	None	None	None	187452233	187463260	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	None	None	None	187452233	187463260	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	None	None	None	187452233	187463260	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	1001	None	None	187452233	187463260	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000470319	retained_intron	KNOWN	None	None	None	None	187452233	187463260	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZNF51	0	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	None	None	None	187453975	187463247	-1	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	None	None	None	187453975	187463247	-1	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	None	None	None	187453975	187463247	-1	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	None	None	None	187453975	187463247	-1	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	1001	None	None	187453975	187463247	-1	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	ENST00000496823	processed_transcript	PUTATIVE	None	None	None	None	187453975	187463247	-1	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	604	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/encode.6celltypes.consensus.bedg.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/genetic_map_HapMapII_GRCh37.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/hg19.gwas.bed.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/hg19_fitcons_fc-i6-0_V1-01.bed.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/hprd_interaction_edges.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl66
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl66	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,30 @@
+B8PSA7	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000169293	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000296280	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F5H2J0	MASP1	MASP1	ENSG00000127241	ENST00000541896	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000169293	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5HYM1	MASP1	MASP1	ENSG00000127241	ENST00000541896	None	None
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000296280	None	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000392472	None	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000541811	None	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl67
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl67	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,30 @@
+B8PSA7	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000450123	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000169293	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000296280	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F5H2J0	MASP1	MASP1	ENSG00000127241	ENST00000541896	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000169293	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5HYM1	MASP1	MASP1	ENSG00000127241	ENST00000541896	None	None
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000296280	None	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000392472	None	None
+Q9NSY8	MASP1	MASP1	ENSG00000127241	ENST00000541811	None	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl68
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl68	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,26 @@
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000450123	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl69
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl69	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,26 @@
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000450123	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl70
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl70	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,25 @@
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000450123	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/kegg_pathways_ensembl71
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/kegg_pathways_ensembl71	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,26 @@
+C9J1C7	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JCS5	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000430339	None	None
+C9JL16	BCL6	BCL6	ENSG00000113916	ENST00000438077	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000425937	None	None
+C9JLU5	MASP1	MASP1	ENSG00000127241	ENST00000439271	None	None
+C9JMA2	MASP1	MASP1	ENSG00000127241	ENST00000392475	None	None
+F8W876	MASP1	MASP1	ENSG00000127241	ENST00000392470	None	None
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000232014	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000406870	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P41182	BCL6	BCL6	ENSG00000113916	ENST00000450123	hsa:604	path:hsa05202;Transcriptional_misregulation_in_cancer
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000169293	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000296280	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000337774	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa04610;Complement_and_coagulation_cascades
+P48740	MASP1	MASP1	ENSG00000127241	ENST00000392472	hsa:5648	path:hsa05150;Staphylococcus_aureus_infection
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04080;Neuroactive_ligand_receptor_interaction
+P61278	SST	SST	ENSG00000157005	ENST00000287641	hsa:6750	path:hsa04971;Gastric_acid_secretion
+Q5QGT7	RTP2	RTP2	ENSG00000198471	ENST00000358241	hsa:344892	None
+Q96DX8	RTP4	RTP4	ENSG00000136514	ENST00000259030	hsa:64108	None
+none	BCL6	BCL6	ENSG00000113916	ENST00000419510	None	None
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz
Binary file test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz.tbi
Binary file test-data/test-cache/gemini/data/stam.125cells.dnaseI.hg19.bed.gz.tbi has changed
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/summary_gene_table_v75
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/gemini/data/summary_gene_table_v75	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,23 @@
+Chromosome	Gene_name	Is_hgnc	Ensembl_gene_id	HGNC_id	Synonyms	Rvis_pct	Strand	Transcript_min_start	Transcript_max_end	Mammalian_phenotype_id
+chr3	None	0	ENSG00000239093	None	None	None	1	187141103	187141207	None
+chr3	None	0	ENSG00000228952	None	None	None	1	187166633	187167238	None
+chr3	None	0	ENSG00000223401	None	None	None	1	187461474	187463208	None
+chr3	MASP	0	ENSG00000127241	None	PRSS5,MASP1,CRARF	16.8141071	-1	186935942	187009810	None
+chr3	PRSS5	0	ENSG00000127241	None	MASP1,CRARF,MASP	16.8141071	-1	186935942	187009810	None
+chr3	MASP1	1	ENSG00000127241	6901	PRSS5,CRARF,MASP	16.8141071	-1	186935942	187009810	None
+chr3	CRARF	0	ENSG00000127241	None	PRSS5,MASP1,MASP	16.8141071	-1	186935942	187009810	None
+chr3	IFRG28	0	ENSG00000136514	None	RTP4,Z3CXXC4	94.35008257	1	187086120	187089864	None
+chr3	RTP4	1	ENSG00000136514	23992	IFRG28,Z3CXXC4	94.35008257	1	187086120	187089864	None
+chr3	Z3CXXC4	0	ENSG00000136514	None	IFRG28,RTP4	94.35008257	1	187086120	187089864	None
+chr3	SST	1	ENSG00000157005	11329	SMST	78.16112291	-1	187386694	187388187	MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3	SMST	0	ENSG00000157005	None	SST	78.16112291	-1	187386694	187388187	MP:0002873,MP:0005386,MP:0005376,MP:0005381,MP:0003631,MP:0005378
+chr3	Z3CXXC2	0	ENSG00000198471	None	RTP2,MGC78665	69.20853975	-1	187416047	187420345	MP:0005389
+chr3	RTP2	1	ENSG00000198471	32486	Z3CXXC2,MGC78665	69.20853975	-1	187416047	187420345	MP:0005389
+chr3	MGC78665	0	ENSG00000198471	None	Z3CXXC2,RTP2	69.20853975	-1	187416047	187420345	MP:0005389
+chr3	None	0	ENSG00000228804	None	None	None	1	187420101	187451637	None
+chr3	ZNF51	0	ENSG00000113916	None	LAZ3,BCL5,BCL6,ZBTB27,BCL6A	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	LAZ3	0	ENSG00000113916	None	BCL5,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL5	0	ENSG00000113916	None	LAZ3,ZNF51,BCL6,ZBTB27,BCL6A	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6A	0	ENSG00000113916	None	LAZ3,ZNF51,BCL6,BCL5,ZBTB27	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	BCL6	1	ENSG00000113916	1001	LAZ3,ZNF51,ZBTB27,BCL5,BCL6A	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
+chr3	ZBTB27	0	ENSG00000113916	None	LAZ3,ZNF51,BCL6,BCL5,BCL6A	23.5727766	-1	187439165	187463515	MP:0005369,MP:0005384,MP:0005376,MP:0005388,MP:0005370,MP:0010768,MP:0002873,MP:0005389,MP:0005378,MP:0005397,MP:0005385,MP:0005387
diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/test-cache/gemini/data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz.tbi
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diff -r ee894347fcd6 -r cdd90678004a test-data/util/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/README.rst	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,25 @@
+Prepare Gemini annotation files and test databases for tool tests
+=================================================================
+
+Each version of GEMINI is tied to a particular set of annotation files and
+database version.
+
+The ``build-gemini-testdata.sh`` script in this folder should be used to
+regenerate the annotation files and the test databases whenever the GEMINI
+version required by the tool wrappers gets upgraded.
+
+The script requires a working GEMINI installation at the targeted version and
+a folder with GEMINI's original annotation files, and can be executed with::
+
+  sh build-gemini-testdata.sh path/to/gemini/annotation/files
+  
+It will regenerate the annotation files inside test-data/test-cache/gemini/data
+and rebuild the *.db files in test-data.
+
+.. Note::
+
+   If the version of GEMINI that you are upgrading to uses a gemini-config.yaml
+   file that is different from the one found in test-data/test-cache you will
+   have to upgrade this file manually (make sure you leave the line
+   ``annotation_dir: gemini/data`` unchanged in the process).
+
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/anno.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/anno.bed	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,3 @@
+chr3	187000000	187150000
+chr3	187150000	187300000
+chr3	187300000	187450000
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/anno.bed.gz
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diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/gemini_load_input.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/gemini_load_input.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.1
+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
+##ALT=<ID=DEL,Description="Deletion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
+##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
+##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
+##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
+##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
+##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
+##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
+##reference=GRCh37
+##SnpEffVersion="SnpEff 3.0f (build 2012-08-23), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  GRCh37.66 -i vcf -o vcf -c /Users/arq5x/src/other/snpEff_3_0/snpEff.config ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	10583	rs58108140	G	A	100.0	PASS	AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1	10611	rs189107123	C	G	100.0	PASS	AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1	13302	rs180734498	C	T	100.0	PASS	THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1	13327	rs144762171	G	C	100.0	PASS	AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
+1	13957	.	TC	T	28.0	PASS	AA=TC;AC=35;AN=2184;VT=INDEL;AVGPOST=0.8711;RSQ=0.2501;LDAF=0.0788;THETA=0.0100;ERATE=0.0065;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1	13980	rs151276478	T	C	100.0	PASS	AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
+1	30923	rs140337953	G	T	100.0	PASS	AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73;EFF=DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER||||177|MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER||||236|MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|)
+1	46402	.	C	CTGT	31.0	PASS	AA=.;RSQ=0.0960;AN=2184;AC=8;VT=INDEL;AVGPOST=0.8325;THETA=0.0121;ERATE=0.0072;LDAF=0.0903;AF=0.0037;ASN_AF=0.0017;AFR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	47190	.	G	GA	192.0	PASS	AA=G;AVGPOST=0.9041;AN=2184;AC=29;VT=INDEL;LDAF=0.0628;THETA=0.0153;RSQ=0.2883;ERATE=0.0041;AF=0.01;AMR_AF=0.0028;AFR_AF=0.06;EFF=INTERGENIC(MODIFIER|||||||||)
+1	51476	rs187298206	T	C	100.0	PASS	ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	51479	rs116400033	T	A	100.0	PASS	RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22;EFF=INTERGENIC(MODIFIER|||||||||)
+1	51914	rs190452223	T	G	100.0	PASS	ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1	51935	rs181754315	C	T	100.0	PASS	THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0;EFF=INTERGENIC(MODIFIER|||||||||)
+1	51954	rs185832753	G	C	100.0	PASS	LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	52058	rs62637813	G	C	100.0	PASS	AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05;EFF=INTERGENIC(MODIFIER|||||||||)
+1	52144	rs190291950	T	A	100.0	PASS	THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	52185	.	TTAA	T	244.0	PASS	AA=.;AN=2184;LDAF=0.0124;VT=INDEL;AC=10;THETA=0.0232;RSQ=0.4271;AVGPOST=0.9840;ERATE=0.0037;AF=0.0046;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1	52238	rs150021059	T	G	100.0	PASS	THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95;EFF=INTERGENIC(MODIFIER|||||||||)
+1	53234	.	CAT	C	227.0	PASS	AA=CAT;AVGPOST=0.9936;AN=2184;VT=INDEL;THETA=0.0119;AC=10;LDAF=0.0074;RSQ=0.6237;ERATE=0.0007;AF=0.0046;AMR_AF=0.0028;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1	54353	rs140052487	C	A	100.0	PASS	THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
+1	54421	rs146477069	A	G	100.0	PASS	ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1	54490	rs141149254	G	A	100.0	PASS	ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15;EFF=INTERGENIC(MODIFIER|||||||||)
+1	54676	rs2462492	C	T	100.0	PASS	LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18;EFF=INTERGENIC(MODIFIER|||||||||)
+1	54753	rs143174675	T	G	100.0	PASS	AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55164	rs3091274	C	A	100.0	PASS	AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55249	.	C	CTATGG	443.0	PASS	AA=C;AVGPOST=0.9073;ERATE=0.0063;RSQ=0.5891;AN=2184;THETA=0.0038;VT=INDEL;AC=151;LDAF=0.0968;AF=0.07;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55299	rs10399749	C	T	100.0	PASS	RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55313	rs182462964	A	T	100.0	PASS	ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55326	rs3107975	T	C	100.0	PASS	AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55330	rs185215913	G	A	100.0	PASS	ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55367	rs190850374	G	A	100.0	PASS	ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55388	rs182711216	C	T	100.0	PASS	THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55394	rs2949420	T	A	100.0	PASS	AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55416	rs193242050	G	A	100.0	PASS	AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55427	rs183189405	T	C	100.0	PASS	THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55816	rs187434873	G	A	100.0	PASS	AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55850	rs191890754	C	G	100.0	PASS	AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
+1	55852	rs184233019	G	C	100.0	PASS	THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013;EFF=INTERGENIC(MODIFIER|||||||||)
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.auto_dom.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_dom.ped	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,9 @@
+1	1_dad	0	0	-1	1
+1	1_mom	0	0	-1	1
+1	1_kid	1_dad	1_mom	-1	2
+2	2_dad	0	0	-1	1
+2	2_mom	0	0	-1	2
+2	2_kid	2_dad	2_mom	-1	2
+3	3_dad	0	0	-1	2
+3	3_mom	0	0	-1	-9
+3	3_kid	3_dad	3_mom	-1	2
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.auto_dom.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_dom.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,127 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr10,length=135534747,assembly=hg19>
+##contig=<ID=chr11,length=135006516,assembly=hg19>
+##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
+##contig=<ID=chr12,length=133851895,assembly=hg19>
+##contig=<ID=chr13,length=115169878,assembly=hg19>
+##contig=<ID=chr14,length=107349540,assembly=hg19>
+##contig=<ID=chr15,length=102531392,assembly=hg19>
+##contig=<ID=chr16,length=90354753,assembly=hg19>
+##contig=<ID=chr17,length=81195210,assembly=hg19>
+##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
+##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
+##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
+##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
+##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
+##contig=<ID=chr18,length=78077248,assembly=hg19>
+##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
+##contig=<ID=chr19,length=59128983,assembly=hg19>
+##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
+##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
+##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
+##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr20,length=63025520,assembly=hg19>
+##contig=<ID=chr21,length=48129895,assembly=hg19>
+##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
+##contig=<ID=chr22,length=51304566,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
+##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
+##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
+##contig=<ID=chr5,length=180915260,assembly=hg19>
+##contig=<ID=chr6,length=171115067,assembly=hg19>
+##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
+##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
+##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
+##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
+##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
+##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
+##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
+##contig=<ID=chr7,length=159138663,assembly=hg19>
+##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
+##contig=<ID=chr8,length=146364022,assembly=hg19>
+##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
+##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
+##contig=<ID=chr9,length=141213431,assembly=hg19>
+##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
+##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
+##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
+##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
+##contig=<ID=chrM,length=16571,assembly=hg19>
+##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
+##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
+##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
+##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
+##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
+##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
+##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
+##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
+##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
+##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
+##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
+##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
+##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
+##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
+##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
+##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
+##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
+##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
+##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
+##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
+##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
+##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
+##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
+##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
+##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
+##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
+##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
+##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
+##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
+##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
+##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
+##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
+##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
+##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
+##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
+##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
+##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
+##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
+##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
+##contig=<ID=chrX,length=155270560,assembly=hg19>
+##contig=<ID=chrY,length=59373566,assembly=hg19>
+##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT">
+##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 test4.vep.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1_dad	1_mom	1_kid	2_dad	2_mom	2_kid	3_dad	3_mom	3_kid
+chr10	1142208	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	1142209	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:59:87.16:940,87,0	0/1:0,29:49:78.20:899,78,0	1/1:0,24:64:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	48003992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:97.16:940,87,0	0/0:0,29:29:98.20:899,78,0	0/1:0,24:24:96.14:729,66,0
+chr10	48004992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135336656	.	G	A	38.34	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.auto_rec.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_rec.ped	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,10 @@
+#family_id	sample_id	paternal_id	maternal_id	sex	phenotype
+1	1_dad	0	0	-1	1
+1	1_mom	0	0	-1	1
+1	1_kid	1_dad	1_mom	-1	2
+2	2_dad	0	0	-1	1
+2	2_mom	0	0	-1	1
+2	2_kid	2_dad	2_mom	-1	2
+3	3_dad	0	0	-1	1
+3	3_mom	0	0	-1	1
+3	3_kid	3_dad	3_mom	-1	2
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.auto_rec.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.auto_rec.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,127 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr10,length=135534747,assembly=hg19>
+##contig=<ID=chr11,length=135006516,assembly=hg19>
+##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
+##contig=<ID=chr12,length=133851895,assembly=hg19>
+##contig=<ID=chr13,length=115169878,assembly=hg19>
+##contig=<ID=chr14,length=107349540,assembly=hg19>
+##contig=<ID=chr15,length=102531392,assembly=hg19>
+##contig=<ID=chr16,length=90354753,assembly=hg19>
+##contig=<ID=chr17,length=81195210,assembly=hg19>
+##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
+##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
+##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
+##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
+##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
+##contig=<ID=chr18,length=78077248,assembly=hg19>
+##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
+##contig=<ID=chr19,length=59128983,assembly=hg19>
+##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
+##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
+##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
+##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr20,length=63025520,assembly=hg19>
+##contig=<ID=chr21,length=48129895,assembly=hg19>
+##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
+##contig=<ID=chr22,length=51304566,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
+##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
+##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
+##contig=<ID=chr5,length=180915260,assembly=hg19>
+##contig=<ID=chr6,length=171115067,assembly=hg19>
+##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
+##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
+##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
+##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
+##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
+##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
+##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
+##contig=<ID=chr7,length=159138663,assembly=hg19>
+##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
+##contig=<ID=chr8,length=146364022,assembly=hg19>
+##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
+##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
+##contig=<ID=chr9,length=141213431,assembly=hg19>
+##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
+##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
+##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
+##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
+##contig=<ID=chrM,length=16571,assembly=hg19>
+##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
+##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
+##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
+##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
+##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
+##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
+##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
+##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
+##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
+##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
+##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
+##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
+##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
+##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
+##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
+##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
+##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
+##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
+##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
+##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
+##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
+##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
+##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
+##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
+##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
+##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
+##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
+##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
+##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
+##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
+##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
+##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
+##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
+##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
+##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
+##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
+##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
+##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
+##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
+##contig=<ID=chrX,length=155270560,assembly=hg19>
+##contig=<ID=chrY,length=59373566,assembly=hg19>
+##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT">
+##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 test4.vep.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1_dad	1_mom	1_kid	2_dad	2_mom	2_kid	3_dad	3_mom	3_kid
+chr10	1142208	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:59:87.16:940,87,0	0/1:0,29:49:78.20:899,78,0	1/1:0,24:64:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	48003992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	48004992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135336656	.	G	A	38.34	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135369532	.	T	C	122.62	.	AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;DP=239;Dels=0.00;FS=5.194;HRun=2;HaplotypeScore=5.7141;MQ=36.02;MQ0=0;MQRankSum=0.082;QD=2.31;ReadPosRankSum=-0.695;CSQ=missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000303903|9/13|benign(0.001)|tolerated(1),missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000432597|10/14|benign(0)|tolerated(1),downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000460441|||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000343131|9/13|benign(0.001)|tolerated(1),intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000171772|SYCE1|ENST00000479535|6/10||,downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000482127|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000130649|CYP2E1|ENST00000368520|6/6||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000368517|9/13|benign(0)|tolerated(1);EFF=DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000460441|),DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000482127|),EXON(MODIFIER|||||CYP2E1|retained_intron|CODING|ENST00000368520|),EXON(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000479535|),INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000368517|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000432597|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|318|SYCE1|protein_coding|CODING|ENST00000303903|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|ENST00000343131|exon_10_135369485_135369551)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0
\ No newline at end of file
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.comp_het.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.comp_het.ped	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,13 @@
+#Family_ID	Individual_ID	Paternal_ID	Maternal_ID	Sex	Phenotype	ethnicity
+1	child_1	dad_1	mom_1	1	2	caucasian
+2	child_2	dad_2	mom_2	1	2	caucasian
+2	dad_2	-9	-9	1	1	caucasian
+2	mom_2	-9	-9	2	1	caucasian
+1	dad_1	-9	-9	1	1	caucasian
+1	mom_1	-9	-9	2	1	caucasian
+3	child_3	dad_3	mom_3	1	2	caucasian
+3	dad_3	-9	-9	1	1	caucasian
+3	mom_3	-9	-9	2	1	caucasian
+4	child_4	dad_4	mom_4	1	2	caucasianNEuropean
+4	dad_4	-9	-9	1	1	caucasianNEuropean
+4	mom_4	-9	-9	2	1	caucasianNEuropean
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.comp_het.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.comp_het.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,120 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=20 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=1,length=249250621,assembly=b37>
+##contig=<ID=10,length=135534747,assembly=b37>
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+##contig=<ID=MT,length=16569,assembly=b37>
+##contig=<ID=X,length=155270560,assembly=b37>
+##contig=<ID=Y,length=59373566,assembly=b37>
+##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta
+##SnpEffVersion="SnpEff 3.2 (build 2013-03-14), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 /if2/arq5x/cphg-quinlan/projects/sms-elsea/varCalling/all.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon  | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	child_1	child_2	dad_2	mom_2	dad_1	mom_1	child_3	dad_3	mom_3	child_4	dad_4	mom_4
+1	16977	.	G	A	2022.88	.	AC=9;AF=0.375;AN=24;BaseQRankSum=-25.424;DP=2999;DS;Dels=0.00;FS=4.077;HRun=0;HaplotypeScore=1.6017;InbreedingCoeff=-0.5953;MQ=10.20;MQ0=124;MQRankSum=0.084;QD=0.90;ReadPosRankSum=0.727;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|7|1)	GT:AD:DP:GQ:PL	0/1:181,69:250:4.24:4,0,401	0/0:190,60:250:5.21:0,5,708	0/1:167,83:250:72.66:73,0,721	0/0:187,63:250:63.12:0,63,633	0/0:221,29:250:96.57:0,97,1729	0/1:160,90:250:99:175,0,537	0/1:177,73:250:99:412,0,723	0/1:183,67:250:99:209,0,838	0/1:174,76:250:99:284,0,844	0/1:194,53:248:26.15:26,0,756	0/1:149,101:250:99:681,0,496	0/1:184,66:250:99:229,0,561
+1	17222	.	A	G	225.47	.	AC=4;AF=0.167;AN=24;BaseQRankSum=-1.725;DP=2985;DS;Dels=0.00;FS=6.073;HRun=0;HaplotypeScore=1.1157;InbreedingCoeff=-0.2212;MQ=14.57;MQ0=605;MQRankSum=-3.790;QD=0.23;ReadPosRankSum=1.860;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1)	GT:AD:DP:GQ:PL	0/0:224,25:250:44.94:0,45,987	0/1:190,44:241:55.80:56,0,776	0/0:230,17:250:90.16:0,90,940	0/1:212,34:250:36.11:36,0,754	0/0:191,55:248:18.04:0,18,1324	0/0:232,17:250:84.90:0,85,1270	0/0:223,27:250:99:0,129,1563	0/0:237,13:250:99:0,107,1537	0/1:207,42:249:99:106,0,1096	0/1:204,43:247:91.42:91,0,1280	0/0:229,20:249:99:0,113,1404	0/0:221,29:250:3.04:0,3,1183
+1	17363	.	TTCT	T	628.85	.	AC=2;AF=0.083;AN=24;BaseQRankSum=4.577;DP=2951;DS;FS=10.112;HRun=0;HaplotypeScore=316.7300;InbreedingCoeff=-0.0909;MQ=22.73;MQ0=27;MQRankSum=1.681;QD=1.33;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|protein_coding|NON_CODING|ENST00000438504|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1)	GT:AD:DP:GQ:PL	0/0:250,0:70:99:0,169,3371	0/0:250,0:78:99:0,199,4105	0/0:250,0:70:99:0,187,3984	0/0:250,0:63:99:0,166,3406	0/0:243,0:89:99:0,262,5364	0/0:250,0:62:99:0,172,3575	0/0:250,0:79:99:0,223,4726	0/0:249,1:80:99:0,181,4749	0/0:234,1:85:99:0,241,5015	0/1:205,27:73:99:371,0,3406	0/1:225,16:74:99:318,0,3528	0/0:250,0:64:99:0,193,3988
+1	17563	.	G	A	79.88	.	AC=1;AF=0.042;AN=24;BaseQRankSum=3.375;DP=3000;DS;Dels=0.00;FS=9.603;HRun=0;HaplotypeScore=0.9909;InbreedingCoeff=-0.0518;MQ=30.15;MQ0=97;MQRankSum=-1.386;QD=0.32;ReadPosRankSum=-0.446;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1)	GT:AD:DP:GQ:PL	0/0:243,7:250:99:0,202,2559	0/0:246,4:250:99:0,187,2479	0/0:250,0:250:99:0,256,3232	0/0:249,1:250:99:0,239,3309	0/0:231,18:250:21.61:0,22,2802	0/0:248,2:250:99:0,214,2657	0/1:232,18:250:99:121,0,1801	0/0:249,1:250:99:0,263,3184	0/0:238,12:250:6.72:0,7,2591	0/0:250,0:250:99:0,343,3875	0/0:247,3:250:99:0,280,3428	0/0:250,0:250:99:0,301,3416
+1	17697	.	G	C	255.3	.	AC=4;AF=0.167;AN=24;BaseQRankSum=-1.815;DP=2999;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.7379;InbreedingCoeff=-0.2256;MQ=15.66;MQ0=86;MQRankSum=2.999;QD=0.26;ReadPosRankSum=-2.160;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1)	GT:AD:DP:GQ:PL	0/1:214,36:250:99:132,0,595	0/0:249,1:250:78.22:0,78,967	0/0:248,1:250:81.24:0,81,1022	0/1:216,34:250:91.94:92,0,404	0/0:226,24:250:56.86:0,57,1099	0/0:245,4:249:23.87:0,24,704	0/0:225,25:250:2.97:0,3,746	0/1:216,33:250:80.80:81,0,810	0/0:245,4:250:73.97:0,74,1201	0/1:222,28:250:12.96:13,0,920	0/0:249,1:250:87.24:0,87,1000	0/0:182,66:250:8.40:0,8,703
+1	17722	.	A	G	32.03	.	AC=3;AF=0.125;AN=24;BaseQRankSum=0.923;DP=2937;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.9343;InbreedingCoeff=-0.1033;MQ=14.33;MQ0=62;MQRankSum=-4.474;QD=0.04;ReadPosRankSum=0.750;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1)	GT:AD:DP:GQ:PL	0/0:247,3:250:51.15:0,51,628	0/0:250,0:250:60.18:0,60,746	0/0:250,0:250:54.17:0,54,685	0/0:249,1:250:54.15:0,54,644	0/0:233,0:233:81.25:0,81,1014	0/0:235,4:239:45.13:0,45,549	0/0:249,0:250:45.13:0,45,514	0/0:249,1:250:78.20:0,78,853	0/0:247,0:247:90.24:0,90,1012	0/1:227,17:244:0.06:0,0,670	0/1:214,11:225:4.62:5,0,542	0/1:236,13:249:71.41:71,0,448
+1	17730	.	C	A	102.87	.	AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|protein_coding|NON_CODING|ENST00000430492|7|1)	GT:AD:DP:GQ:PL	0/0:246,4:250:36.11:0,36,464	0/0:244,5:249:57.17:0,57,727	0/0:244,6:250:48.15:0,48,628	0/0:247,3:250:51.13:0,51,621	0/1:242,8:250:26.26:26,0,830	0/0:246,4:250:48.14:0,48,601	0/1:238,11:250:48.54:49,0,386	0/0:244,5:249:42.12:0,42,491	0/0:239,3:243:23.74:0,24,609	0/1:221,13:234:13.85:14,0,482	0/1:232,11:243:7:7,0,501	0/1:238,12:250:73.18:73,0,368
+1	17746	.	A	G	607.7	.	AC=8;AF=0.333;AN=24;BaseQRankSum=13.191;DP=2993;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.4155;InbreedingCoeff=-0.5280;MQ=11.87;MQ0=5;MQRankSum=-4.672;QD=0.30;ReadPosRankSum=3.574;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|3|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|3|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|3|1)	GT:AD:DP:GQ:PL	0/0:206,44:250:7.45:0,7,373	0/0:221,29:250:5.12:0,5,468	0/0:224,26:250:3.61:0,4,382	0/0:216,34:250:9.49:0,9,405	0/1:243,7:250:43.06:43,0,781	0/1:195,55:250:99:113,0,232	0/1:218,32:250:44.30:44,0,212	0/1:219,31:250:0.03:0,0,330	0/1:211,39:250:74.42:74,0,236	0/1:209,34:243:68.40:68,0,298	0/1:172,77:249:99:193,0,137	0/1:219,30:250:99:137,0,197
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.de_novo.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.de_novo.ped	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,9 @@
+1	1_dad	0	0	-1	1
+1	1_mom	0	0	-1	1
+1	1_kid	1_dad	1_mom	-1	2
+2	2_dad	0	0	-1	1
+2	2_mom	0	0	-1	1
+2	2_kid	2_dad	2_mom	-1	2
+3	3_dad	0	0	-1	1
+3	3_mom	0	0	-1	1
+3	3_kid	3_dad	3_mom	-1	2
\ No newline at end of file
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-data/test.de_novo.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-data/test.de_novo.vcf	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,127 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr10,length=135534747,assembly=hg19>
+##contig=<ID=chr11,length=135006516,assembly=hg19>
+##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
+##contig=<ID=chr12,length=133851895,assembly=hg19>
+##contig=<ID=chr13,length=115169878,assembly=hg19>
+##contig=<ID=chr14,length=107349540,assembly=hg19>
+##contig=<ID=chr15,length=102531392,assembly=hg19>
+##contig=<ID=chr16,length=90354753,assembly=hg19>
+##contig=<ID=chr17,length=81195210,assembly=hg19>
+##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
+##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
+##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
+##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
+##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
+##contig=<ID=chr18,length=78077248,assembly=hg19>
+##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
+##contig=<ID=chr19,length=59128983,assembly=hg19>
+##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
+##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
+##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
+##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr20,length=63025520,assembly=hg19>
+##contig=<ID=chr21,length=48129895,assembly=hg19>
+##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
+##contig=<ID=chr22,length=51304566,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
+##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
+##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
+##contig=<ID=chr5,length=180915260,assembly=hg19>
+##contig=<ID=chr6,length=171115067,assembly=hg19>
+##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
+##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
+##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
+##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
+##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
+##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
+##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
+##contig=<ID=chr7,length=159138663,assembly=hg19>
+##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
+##contig=<ID=chr8,length=146364022,assembly=hg19>
+##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
+##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
+##contig=<ID=chr9,length=141213431,assembly=hg19>
+##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
+##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
+##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
+##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
+##contig=<ID=chrM,length=16571,assembly=hg19>
+##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
+##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
+##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
+##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
+##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
+##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
+##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
+##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
+##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
+##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
+##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
+##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
+##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
+##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
+##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
+##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
+##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
+##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
+##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
+##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
+##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
+##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
+##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
+##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
+##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
+##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
+##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
+##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
+##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
+##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
+##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
+##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
+##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
+##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
+##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
+##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
+##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
+##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
+##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
+##contig=<ID=chrX,length=155270560,assembly=hg19>
+##contig=<ID=chrY,length=59373566,assembly=hg19>
+##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT">
+##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 test4.vep.vcf "
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1_dad	1_mom	1_kid	2_dad	2_mom	2_kid	3_dad	3_mom	3_kid
+chr10	1142208	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,23:24:66.14:729,66,0	0/0:1,37:59:87.16:940,87,0	0/0:0,29:49:78.20:899,78,0	0/0:0,22:64:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0
+chr10	48003992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,23:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,23:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,23:24:66.14:729,66,0
+chr10	48004992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056)	GT:AD:DP:GQ:PL	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,23:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	1/1:0,23:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,23:24:66.14:729,66,0
+chr10	135336656	.	G	A	38.34	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0	0/1:1,37:39:87.16:940,87,0	0/1:0,29:29:78.20:899,78,0	0/1:0,24:24:66.14:729,66,0
+chr10	135369532	.	T	C	122.62	.	AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;DP=239;Dels=0.00;FS=5.194;HRun=2;HaplotypeScore=5.7141;MQ=36.02;MQ0=0;MQRankSum=0.082;QD=2.31;ReadPosRankSum=-0.695;CSQ=missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000303903|9/13|benign(0.001)|tolerated(1),missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000432597|10/14|benign(0)|tolerated(1),downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000460441|||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000343131|9/13|benign(0.001)|tolerated(1),intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000171772|SYCE1|ENST00000479535|6/10||,downstream_gene_variant|||ENSG00000171772|SYCE1|ENST00000482127|||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000130649|CYP2E1|ENST00000368520|6/6||,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000368517|9/13|benign(0)|tolerated(1);EFF=DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000460441|),DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000482127|),EXON(MODIFIER|||||CYP2E1|retained_intron|CODING|ENST00000368520|),EXON(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000479535|),INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000368517|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000432597|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|318|SYCE1|protein_coding|CODING|ENST00000303903|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|ENST00000343131|exon_10_135369485_135369551)	GT:AD:DP:GQ:PL	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,22:24:66.14:729,66,0	0/0:1,37:39:87.16:940,87,0	0/0:0,29:29:78.20:899,78,0	0/1:0,21:24:66.14:729,66,0	0/0:1,37:50:87.16:940,87,0	0/0:0,29:50:78.20:899,78,0	0/1:0,24:50:66.14:729,66,0
diff -r ee894347fcd6 -r cdd90678004a test-data/util/build-gemini-testdata.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-gemini-testdata.sh	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,72 @@
+cd "$(dirname "$0")"
+
+export GEMINI_CONFIG=../test-cache
+OUT_PTH=$GEMINI_CONFIG/gemini/data
+GENOMIC_REGION=3:187000000-187500000
+
+
+if [ -n "$1" ]; then
+
+IN_PTH="$1"
+# downsample all vcf and bed annotation files to the region of interest and reindex
+for vcf in `ls $IN_PTH/*.gz | grep -v hprd_interaction_edges.gz -`
+do
+    python ./shrink_tabix.py $vcf -r $GENOMIC_REGION -o $OUT_PTH/`basename $vcf`
+done
+
+# downsample gene_table files to the region of interest
+echo "$IN_PTH/summary_gene_table_v75 -> $OUT_PTH/summary_gene_table_v75"
+python ./shrink_simple_tab.py $IN_PTH/summary_gene_table_v75 -r chr$GENOMIC_REGION -c 0 8 9 -n 1 -o $OUT_PTH/summary_gene_table_v75
+
+echo "$IN_PTH/detailed_gene_table_v75 -> $OUT_PTH/detailed_gene_table_v75"
+python ./shrink_simple_tab.py $IN_PTH/detailed_gene_table_v75 -r chr$GENOMIC_REGION -c 0 11 12 -n 1 -o $OUT_PTH/detailed_gene_table_v75
+
+# filter kegg_pathway files to retain only records of the genes listed
+# in the downsampled summary_gene_table
+for kegg in `ls $IN_PTH/kegg_pathways_*`
+do
+    echo "$kegg -> $OUT_PTH/`basename $kegg`"
+    cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Fwf - $kegg > $OUT_PTH/`basename $kegg`
+done
+
+# filter hprd_interaction file to retain only records of the genes listed
+# in the downsampled summary_gene_table
+echo "$IN_PTH/hprd_interaction_edges.gz -> $OUT_PTH/hprd_interaction_edges.gz"
+bgzip -dc $IN_PTH/hprd_interaction_edges.gz > $OUT_PTH/hprd_interaction_edges
+cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Ff - $OUT_PTH/hprd_interaction_edges | bgzip > $OUT_PTH/hprd_interaction_edges.gz
+rm $OUT_PTH/hprd_interaction_edges
+
+# filter cancer_gene_census file to retain only records of the genes listed
+# in the downsampled summary_gene_table;
+# TO DO: make the filter stricter by looking for matches only in the first
+# column of the cancer_gene_census file (but the file is relatively small anyway)
+echo "$IN_PTH/cancer_gene_census.20140120.tsv -> $OUT_PTH/cancer_gene_census.20140120.tsv"
+cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Fwf - $IN_PTH/cancer_gene_census.20140120.tsv > $OUT_PTH/cancer_gene_census.20140120.tsv
+
+else
+    echo "no path to gemini annotation files provided - only building test databases"
+fi
+
+
+# now use gemini load to build the test databases
+echo "Building gemini test databases"
+echo "Test databases for gemini_load"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/gemini_load_input.vcf -t snpEff ../gemini_load_result1.db
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/gemini_load_input.vcf -t snpEff --skip-gene-tables --no-load-genotypes ../gemini_load_result2.db
+echo "Test database for gemini_amend"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_rec.vcf -t snpEff ../gemini_amend_input.db
+echo "Test database for gemini_annotate"
+bgzip -c build-data anno.bed > build-data/anno.bed.gz
+tabix --force -p bed build-data/anno.bed.gz
+cp ../gemini_load_result1.db ../gemini_annotate_result.db
+gemini --annotation-dir $OUT_PTH annotate -f build-data/anno.bed.gz -c anno5 -a count ../gemini_annotate_result.db
+echo "Test database for gemini_set_somatic"
+cp ../gemini_load_result1.db ../gemini_is_somatic_result.db
+gemini set_somatic --min-somatic-score 5.65 ../gemini_is_somatic_result.db
+echo "Test database for gemini_de_novo and gemini_mendel_errors"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.de_novo.vcf -p build-data/test.de_novo.ped -t snpEff ../gemini_de_novo_input.db
+echo "Test database for gemini_comp_hets"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.comp_het.vcf -p build-data/test.comp_het.ped -t snpEff ../gemini_comphets_input.db
+echo "Test databases for gemini_autosomal"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_rec.vcf -p build-data/test.auto_rec.ped -t snpEff ../gemini_auto_rec_input.db
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_dom.vcf -p build-data/test.auto_dom.ped -t snpEff ../gemini_auto_dom_input.db
diff -r ee894347fcd6 -r cdd90678004a test-data/util/shrink_simple_tab.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/shrink_simple_tab.py	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,61 @@
+from __future__ import print_function
+
+import argparse
+from functools import partial
+
+
+def keep_line(line, pos_cols, region):
+    fields = line.rstrip().split(b'\t')
+    if fields[pos_cols[0]] == region[0]:  # same chromosome
+        if (
+            region[1] < int(fields[pos_cols[1]]) < region[2]
+        ) or (
+            region[1] < int(fields[pos_cols[2]]) < region[2]
+        ):
+            return True
+
+
+def main(infile, ofile, num_header_lines):
+    print(infile, '->', ofile)
+    with open(infile, 'rb') as i:
+        with open(ofile, 'wb') as o:
+            # copy header lines
+            for c in range(num_header_lines):
+                o.write(next(i))
+            for line in i:
+                if keep_line(line):
+                    o.write(line)
+
+
+if __name__ == '__main__':
+    p = argparse.ArgumentParser()
+    p.add_argument('infile')
+    p.add_argument(
+        '-r', '--region',
+        required=True,
+        help='the region of the input file to rewrite'
+    )
+    p.add_argument(
+        '-o', '--ofile',
+        required=True,
+        help="the name of the output file"
+    )
+    p.add_argument(
+        '-c', '--cols',
+        nargs=3, type=int, required=True,
+        help="the columns of the input file specifying chrom, start and stop, "
+             "respectively"
+    )
+    p.add_argument(
+        '-n', '--num-header-lines',
+        type=int, default=0,
+        help='the number of header lines present in the input; These will '
+             'always be copied over to the new file.'
+    )
+    args = vars(p.parse_args())
+
+    chrom, reg = args['region'].split(':')
+    region = [chrom.encode()] + [int(x) for x in reg.split('-')]
+    keep_line = partial(keep_line, pos_cols=args['cols'], region=region)
+
+    main(args['infile'], args['ofile'], args['num_header_lines'])
diff -r ee894347fcd6 -r cdd90678004a test-data/util/shrink_tabix.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/shrink_tabix.py	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,42 @@
+from __future__ import print_function
+
+import argparse
+
+import pysam
+
+
+def main(infile, ofile, region):
+    print(infile, '->', ofile)
+    with pysam.Tabixfile(infile) as i:
+        fformat = i.format.lower()
+        if fformat == 'sam':
+            fformat = 'bed'
+        if ofile[-3:] == '.gz':
+            ofile = ofile[:-3]
+        with open(ofile, 'w') as o:
+            try:
+                region_it = i.fetch(region=region)
+            except ValueError:
+                region_it = i.fetch(region='chr' + region)
+            for line in i.header:
+                o.write(line + '\n')
+            for line in region_it:
+                o.write(str(line) + '\n')
+    pysam.tabix_index(ofile, preset=fformat, force=True)
+
+
+if __name__ == '__main__':
+    p = argparse.ArgumentParser()
+    p.add_argument('infile')
+    p.add_argument(
+        '-r', '--region',
+        required=True,
+        help='the region of the input file to rewrite'
+    )
+    p.add_argument(
+        '-o', '--ofile',
+        required=True,
+        help="the name of the output file"
+    )
+    args = vars(p.parse_args())
+    main(**args)
diff -r ee894347fcd6 -r cdd90678004a tool-data/gemini_databases.loc.sample
--- a/tool-data/gemini_databases.loc.sample	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-## GEMINI databases
-#Version	dbkey	Description	Path
-#08_08_2014	hg19	Database (08-08-2014)	/path/to/data
diff -r ee894347fcd6 -r cdd90678004a tool-data/gemini_versioned_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_versioned_databases.loc.sample	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,3 @@
+## GEMINI versioned databases
+#DownloadDate	dbkey	DBversion	Description	Path
+#2018-07-08	hg19	181	GEMINI annotations (2018-07-08 snapshot)	/path/to/data
diff -r ee894347fcd6 -r cdd90678004a tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Oct 17 13:33:53 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Dec 14 12:47:19 2018 -0500
@@ -1,7 +1,7 @@
 <tables>
-    <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gemini_databases.loc" />
+    <table name="gemini_versioned_databases" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, version, name, path</columns>
+        <file path="tool-data/gemini_versioned_databases.loc" />
     </table>
 </tables>
 
diff -r ee894347fcd6 -r cdd90678004a tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Dec 14 12:47:19 2018 -0500
@@ -0,0 +1,8 @@
+<tables>
+    <!-- Location of gemini annotation files for testing -->
+    <table name="gemini_versioned_databases" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, version, name, path</columns>
+        <file path="${__HERE__}/test-data/gemini_versioned_databases.loc" />
+    </table>
+</tables>
+
diff -r ee894347fcd6 -r cdd90678004a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 17 13:33:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="gemini" version="0.18.1">
-        <repository changeset_revision="49de32b47548" name="package_gemini_0_18_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="tabix" version="0.2.6">
-        <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>