# HG changeset patch
# User iuc
# Date 1598348479 14400
# Node ID 2975b29bcaa199917042e9ea09284eea9de2e6b3

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"

diff -r 000000000000 -r 2975b29bcaa1 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,24 @@
+<macros>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">1.7.0</token>
+    <xml name="ref_select">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file">
+                <option value="cached" selected="True">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Reference Genome File">
+                    <options from_data_table="fasta_indexes"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" format="fasta" type="data" label="Reference Genome File" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="input_default">
+        <param name="tumor" type="data" format="bam" label="Tumor file" />
+        <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
+    </xml>
+</macros>
diff -r 000000000000 -r 2975b29bcaa1 test-data/all_variants_paired.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_variants_paired.vcf	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,111 @@
+##fileformat=VCFv4.1
+##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
+##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
+##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
+##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">
+##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">
+##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
+##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
+##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
+##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
+##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
+##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
+##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
+##FILTER=<ID=Bias,Description="Strand Bias">
+##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
+##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">
+##FILTER=<ID=d5,Description="Total Depth < 5">
+##FILTER=<ID=v3,Description="Var Depth < 3">
+##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
+##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">
+##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
+##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
+##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
+##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
+##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
+##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">
+##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">
+##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">
+##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
+##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
+##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
+##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
+##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
+##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
+##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
+##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
+##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
+##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
+##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
+##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
+##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
+##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Tumor	Normal
+chrM	150	.	T	C	121	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:40.5:1:1:0:60:4:1:0:1.5	1/1:9:9:4,5:0,0:0,9:1:0,2:29.8:1:38.4:1:1:0:60:18:1:0.1111:1.8
+chrM	195	.	C	T	120	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:40:0:1:0:60:2:1:0:2	1/1:9:9:3,6:0,0:0,9:1:0,2:21.9:1:37.9:1:1:0:60:18:1:0:1.8
+chrM	295	.	C	T	75	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCATAACAAAAAATTT;RSEQ=CACCAAACCCCCCCCTCCCC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:4:4:4,0:0,0:0,4:1:0,0:19.5:1:37.5:1:1:0:60:8:1:0:2.2
+chrM	302	.	AC	A	85	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6
+chrM	410	.	A	T	149	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:36.7:1:1:0:60:6:1:0.3333:2.3	1/1:18:18:12,6:0,0:0,18:1:0,2:19.7:1:35.9:1:1:0:60:17:1:0.0556:1.9
+chrM	464	.	C	T	193	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=Inf;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1	1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2
+chrM	491	.	T	C	228	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=Inf;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7	1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7
+chrM	681	.	C	T	30	v3	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02084;SOR=Inf;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:2:1,1:70,52:122,2:0.0161:2,2:36:1:30.5:1:1:1.34287:49:4:0.0163:0:1	0/0:732:0:0,0:418,314:732,0:0:2,0:25:1:37.4:1:1:0:54.8:60:1:0:0.1
+chrM	692	.	T	C	38	v3	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02079;SOR=Inf;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:2:1,1:73,49:122,2:0.0161:2,2:36:1:38:1:1:1.48485:49:4:0.0163:0:1	0/0:733:0:0,0:419,314:733,0:0:2,0:24.6:1:37.1:1:1:0:54.9:121.167:1:0:0.1
+chrM	737	.	A	G	30	v3	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=106;VD=2;AF=0.0189;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02224;SOR=Inf;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:106:2:1,1:42,61:103,2:0.0189:2,2:14.5:1:30.5:1:1:1.45:60:4:0.0202:0.0094:1	0/0:602:0:0,0:228,374:602,0:0:2,0:27.9:1:34.8:1:1:0:59.2:15.27:1:0:0.1
+chrM	1735	.	C	T	140	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:1,2:0,0:0,3:1:0,2:46.7:1:40.3:1:1:0:60:6:1:0:1	1/1:14:14:6,8:0,0:0,14:1:0,2:26:1:37:1:1:0:60:28:1:0:1.1
+chrM	2354	.	C	T	135	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:36.5:1:1:0:60:6:1:0.3333:1	1/1:11:11:8,3:0,0:0,11:1:0,2:23.1:1:39.1:1:1:0:60:22:1:0.0909:1.3
+chrM	2395	.	C	A	35	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62857;SOR=0;LSEQ=AACAGCCCAATATCTACAAT;RSEQ=AACCAACAAGTCATTATTAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:22.3:1:36.7:1:1:0:60:6:1:0:1	0/1:12:2:1,1:5,5:10,2:0.1667:2,2:42:1:35:1:1:1:60:4:0.1667:0:1.5
+chrM	2485	.	C	T	123	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53.3:6:1:0:1	1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40.2:5.5:1:0:1.2
+chrM	2493	.	C	T	32	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81429;SOR=0;LSEQ=GAACTCGGCAAACCTTACCC;RSEQ=GCCTGTTTACCAAAAACATC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:37:1:1:0:50:4:1:0:1	0/1:19:2:1,1:10,7:17,2:0.1053:2,2:42:1:32.5:1:1:1.40151:13:4:0.1053:0:2
+chrM	3012	.	G	A	99	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58.2:12:1:0:1.2
+chrM	3394	.	C	T	35	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCGAACGAAAAATTCTAGG;RSEQ=TATATACAACTACGCAAAGG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:14:2:1,1:7,5:12,2:0.1429:2,2:25.5:1:35.5:1:1:1.36624:60:4:0.1429:0:1
+chrM	3588	.	C	A	32	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.62857;SOR=0;LSEQ=CCCCCTCCCCATACCCAACC;RSEQ=CCTGGTCAACCTCAACCTAG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:2,1:3,0:0:2,0:15.7:1:39.7:1:1:0:60:6:1:0:0	0/1:12:2:1,1:5,5:10,2:0.1667:2,2:28:1:32.5:1:1:1:60:4:0.1667:0:1
+chrM	5581	.	C	T	133	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:33.6:24:1:0.0833:1
+chrM	6720	.	T	C	75	d5	STATUS=SampleSpecific;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:25:1:37.5:1:1:0:56:8:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
+chrM	7877	.	C	T	34	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.85979;SOR=0;LSEQ=AACGATCCCTCCCTTACCAT;RSEQ=AAATCAATTGGCCACCAATG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:18:1:37.5:1:1:0:60:4:1:0:0	0/1:26:2:1,1:12,12:24,2:0.0769:2,2:24.5:1:34:1:1:1:60:4:0.0769:0:1
+chrM	8270	.	G	A	54	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCGTATTTACCCTATA;RSEQ=CACCCCCTCTACCCCCTCTA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:3:3:1,2:0,0:0,3:1:0,2:12.7:1:34.3:1:1:0:60:6:1:0:1
+chrM	8702	.	G	A	126	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:34:1:1:0:60:4:1:0:1.5	1/1:11:11:6,5:0,0:0,11:1:0,2:25.2:1:36.7:1:1:0:51:22:1:0:1
+chrM	9378	.	G	A	110	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1	1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44.3:8:1:0.1111:1.2
+chrM	9541	.	C	T	58	d5;v3	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:37:1:1:0:60:4:1:0:1	1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:37:1:1:0:60:6:1:0:1
+chrM	10874	.	C	T	37	d5;v3	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:37.5:1:1:0:60:4:1:0:1	1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:37.8:1:1:0:60:4:1:0.5:1
+chrM	11018	.	C	T	84	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51.2:10:1:0:1.2
+chrM	11198	.	C	A	31	v3	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12;SOR=Inf;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:9:2:1,1:3,4:7,2:0.2222:2,2:31.5:1:31.5:1:1:1.29:60:4:0.2222:0:1.5	0/0:16:0:0,0:10,6:16,0:0:2,0:26.3:1:37.2:1:1:0:60:32:1:0:0.5
+chrM	11252	.	A	G	150	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:1,4:0,0:0,5:1:0,2:26.2:1:37.4:1:1:0:60:10:1:0.2:1.2	1/1:17:17:9,8:0,0:0,17:1:0,2:27.8:1:36.9:1:1:0:60:34:1:0.0588:1.2
+chrM	11464	.	T	A	32	PASS	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1	0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2
+chrM	11492	.	A	G	33	v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40441;SOR=0;LSEQ=CTAGGCGGCTATGGTATAAT;RSEQ=CGCCTCACACTCATTCTCAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:3,3:6,0:0:2,0:33.8:1:33.5:1:1:0:60:12:1:0:0.3	0/1:11:2:1,1:5,4:9,2:0.1818:2,2:23:1:33:1:1:1.22474:60:4:0.1818:0.0909:1
+chrM	11723	.	C	T	144	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50.4:32:1:0:1
+chrM	12613	.	A	G	106	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3
+chrM	12706	.	T	C	97	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:40:0:1:0:60:2:1:0:1	1/1:6:6:4,2:0,0:0,6:1:0,2:28.7:1:37.7:1:1:0:60:12:1:0:1.3
+chrM	12851	.	G	A	141	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:22.5:1:36.5:1:1:0:60:8:1:0:1	1/1:14:14:7,7:0,0:0,14:1:0,2:26.2:1:37.2:1:1:0:60:28:1:0:1.1
+chrM	13591	.	G	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63158;SOR=0;LSEQ=ACTCTCATCGCTACCTCCCT;RSEQ=ACAAGCGCCTATAGCACTCG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:17.2:1:34.5:1:1:0:60:8:1:0:0	0/1:16:2:1,1:7,7:14,2:0.125:2,2:17.5:1:37.5:1:1:1:60:4:0.125:0:2
+chrM	13618	.	T	C	38	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.66912;SOR=0;LSEQ=GCCTATAGCACTCGAATAAT;RSEQ=CTTCTCACCCTAACAGGTCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:2,1:3,0:0:2,0:16:1:35.3:1:1:0:60:6:1:0:0.3	0/1:14:2:1,1:4,8:12,2:0.1429:2,2:44.5:1:38.5:1:1:1.90:60:4:0.1429:0:2
+chrM	13709	.	G	A	103	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1	1/1:7:7:3,4:0,0:0,7:1:0,2:22.3:1:36.7:1:1:0:60:14:1:0:1
+chrM	14213	.	C	T	130	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58.1:22:1:0:1.2
+chrM	14581	.	G	A	141	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:43.6:10:1:0:1	1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56.3:14:1:0.0667:1
+chrM	14794	.	A	G	37	PASS	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1	0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0
+chrM	14906	.	A	G	177	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:9:9:5,4:0,0:0,9:1:0,2:28.8:1:34.1:1:1:0:60:8:1:0.1111:2.1	1/1:33:33:15,18:0,0:0,33:1:0,2:22.5:1:35.2:1:1:0:60:66:1:0.0606:1.8
+chrM	14928	.	A	G	181	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=Inf;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1	1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8
+chrM	15302	.	A	G	128	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:38:1:1:0:60:4:1:0:1	1/1:11:11:4,7:0,0:0,11:1:0,2:31.2:1:37.1:1:1:0:60:22:1:0:1.2
+chrM	15453	.	C	A	83	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1
+chrM	15933	.	C	T	57	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTTGTAAACCGGAGA;RSEQ=GAAAACCTTTTTCCAAGGAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:36:1:1:0:60:6:1:0:1
+chrM	16070	.	C	T	107	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7
+chrM	16127	.	T	C	85	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5	1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2
+chrM	16146	.	G	A	106	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGGTACCATAAATACTT;RSEQ=ACCACCTGTAGTACATAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5	1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9
+chrM	16173	.	C	T	120	d5;v3;NM5.25	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTACATAAAAACCCAA;RSEQ=CCACATCAAACCCCCCCCCC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:37.5:1:1:0:60:4:1:0:5.5	1/1:10:10:6,4:0,0:0,10:1:0,2:26.6:1:36.2:1:1:0:60:20:1:0:5.4
+chrM	16184	.	CC	A	121	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42308;SOR=0.2582;LSEQ=AAAACCCAACCCACATCAAA;RSEQ=CCCCCCCCCCATGCTTACAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:1,0:0,0:0,1:0.5:0,0:27:0:39:0:1:0:60:2:1:0:4	1/1:11:9:7,2:0,0:0,9:0.8182:0,2:28.2:1:38.2:1:1:0:60:18:0.9:0.1818:4.6
+chrM	16191	.	C	T	124	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33.5:1:1:0:60:4:1:0:5.5	1/1:12:12:7,5:0,0:0,12:1:0,2:29.6:1:34.7:1:1:0:60:11:1:0.0833:5.2
+chrM	16224	.	CT	TC	159	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.12566;LSEQ=AAGCAAGTACAGCAATCAAC;RSEQ=TCAACTATCACACATCAACT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5	1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2
+chrM	16263	.	C	T	158	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3	1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5
+chrM	16322	.	T	C	125	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5	1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5
+chrM	16521	.	C	T	113	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1	1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1
diff -r 000000000000 -r 2975b29bcaa1 test-data/all_variants_single.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_variants_single.vcf	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,91 @@
+##fileformat=VCFv4.1
+##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
+##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
+##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">
+##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">
+##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
+##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
+##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
+##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
+##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
+##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
+##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
+##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
+##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
+##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
+##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
+##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">
+##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
+##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
+##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
+##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">
+##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">
+##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don't work">
+##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don't match">
+##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">
+##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">
+##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">
+##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">
+##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">
+##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
+##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">
+##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
+##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
+##FILTER=<ID=Bias,Description="Strand Bias">
+##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
+##FILTER=<ID=d3,Description="Total Depth < 3">
+##FILTER=<ID=v2,Description="Var Depth < 2">
+##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
+##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">
+##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
+##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">
+##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">
+##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp">
+##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)">
+##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
+##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
+chrM	150	.	T	C	40	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:2;PMEAN=35;PSTD=1;QUAL=40.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:0,2
+chrM	410	.	A	T	58	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=3:0;PMEAN=23.3;PSTD=1;QUAL=36.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;NM=2.3;HICNT=3;HICOV=3;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:3,0
+chrM	464	.	C	T	108	PASS	SAMPLE=Sample;TYPE=SNV;DP=8;VD=8;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=6:2;PMEAN=22.8;PSTD=1;QUAL=36.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=16;HIAF=1.0000;ADJAF=0;SHIFT3=2;MSI=3;MSILEN=1;NM=2.1;HICNT=8;HICOV=8;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:8:8:0,8:1:0,0:6,2
+chrM	491	.	T	C	127	PASS	SAMPLE=Sample;TYPE=SNV;DP=10;VD=10;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=8:2;PMEAN=28.3;PSTD=1;QUAL=38.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=20;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.7;HICNT=10;HICOV=10;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:10:10:0,10:1:0,0:8,2
+chrM	681	.	C	T	30	PASS	SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=70:52;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.34287;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:124:2:122,2:0.0161:70,52:1,1
+chrM	692	.	T	C	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=73:49;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=1.48485;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:124:2:122,2:0.0161:73,49:1,1
+chrM	737	.	A	G	30	PASS	SAMPLE=Sample;TYPE=SNV;DP=106;VD=2;AF=0.0189;BIAS=2:2;REFBIAS=42:61;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.44707329426235;MQ=60;SN=4;HIAF=0.0202;ADJAF=0.0094;SHIFT3=1;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=99;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:106:2:103,2:0.0189:42,61:1,1
+chrM	1735	.	C	T	63	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:2;PMEAN=46.7;PSTD=1;QUAL=40.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=3;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:1,2
+chrM	2354	.	C	T	57	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=18.3;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=4;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:2,1
+chrM	2485	.	C	T	59	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=17.7;PSTD=1;QUAL=37.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=53.3;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:2,1
+chrM	6720	.	T	C	75	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=56;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	8702	.	G	A	34	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=46;PSTD=1;QUAL=34;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	9378	.	G	A	57	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:3;PMEAN=20.3;PSTD=1;QUAL=36;QSTD=1;SBF=1;ODDRATIO=0;MQ=46;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:0,3
+chrM	9541	.	C	T	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=48.5;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	10874	.	C	T	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=30;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=5;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	11198	.	C	A	31	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=2;AF=0.2222;BIAS=2:2;REFBIAS=3:4;VARBIAS=1:1;PMEAN=31.5;PSTD=1;QUAL=31.5;QSTD=1;SBF=1;ODDRATIO=1.29098889749548;MQ=60;SN=4;HIAF=0.2222;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=2;NM=1.5;HICNT=2;HICOV=9;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:9:2:7,2:0.2222:3,4:1,1
+chrM	11252	.	A	G	86	PASS	SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:4;PMEAN=26.2;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=10;HIAF=1.0000;ADJAF=0.2;SHIFT3=0;MSI=2;MSILEN=1;NM=1.2;HICNT=5;HICOV=5;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:5:5:0,5:1:0,0:1,4
+chrM	11464	.	T	A	32	PASS	SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=25.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:6:2:4,2:0.3333:2,2:1,1
+chrM	12851	.	G	A	73	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=22.5;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	13709	.	G	A	32	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	14581	.	G	A	86	PASS	SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:5:5:0,5:1:0,0:3,2
+chrM	14794	.	A	G	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:6:2:4,2:0.3333:2,2:1,1
+chrM	14906	.	A	G	108	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:9:9:0,9:1:0,0:5,4
+chrM	14928	.	A	G	122	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:9:9:0,9:1:0,0:5,4
+chrM	15302	.	A	G	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16173	.	C	T	37	NM5.25	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=22;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=5.5;HICNT=2;HICOV=2;LSEQ=TGTAGTACATAAAAACCCAA;RSEQ=CCACATCAAACCCCCCCCCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16191	.	C	T	33	NM5.25	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=22;PSTD=1;QUAL=33.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=12;MSILEN=1;NM=5.5;HICNT=2;HICOV=2;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16263	.	C	T	68	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	16322	.	T	C	33	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16521	.	C	T	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
diff -r 000000000000 -r 2975b29bcaa1 test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+test_buildid	hg17	test_displayname	${__HERE__}/genome.fasta
diff -r 000000000000 -r 2975b29bcaa1 test-data/genome.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,333 @@
+>chrM
+NNNCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
+TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
+GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
+CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
+TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA
+TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC
+GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
+CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA
+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA
+ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC
+AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG
+GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC
+ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT
+TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC
+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT
+TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA
+CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC
+ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC
+CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA
+GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA
+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC
+TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT
+AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG
+TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT
+ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT
+GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC
+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA
+GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG
+AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT
+CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC
+CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG
+CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA
+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT
+CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA
+GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC
+GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT
+ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT
+TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG
+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA
+GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA
+AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT
+GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA
+TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA
+GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA
+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG
+GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT
+TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC
+CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca
+taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt
+tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg
+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA
+ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA
+TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA
+GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT
+CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC
+CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT
+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA
+TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT
+CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC
+TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT
+TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg
+taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct
+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA
+TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA
+CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC
+CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA
+CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC
+GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT
+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT
+CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC
+GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT
+CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC
+TTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTG
+GCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT
+CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAAT
+ACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATT
+ATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGA
+CGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTAC
+TTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGC
+TACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT
+AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC
+CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT
+AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac
+ccatccctgagaatccaaaattctccgtgccacctatcacaccccatcct
+aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG
+GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC
+TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATT
+TTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTC
+TAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTC
+CTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAA
+CAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACT
+CATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC
+TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGG
+CCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACC
+AAATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTA
+TCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAA
+AATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTC
+TACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC
+CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGAC
+CCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAA
+TTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTT
+TTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCAT
+CATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACC
+TACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC
+GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCC
+CACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATAC
+TAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAG
+CCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAA
+ACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAA
+GCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC
+TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAA
+AAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCA
+ATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTG
+TCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCC
+ACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTG
+GAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT
+CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGG
+TAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAA
+TCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTA
+GTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAA
+CATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTG
+CTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA
+GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTC
+CTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCA
+CAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCC
+CTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCT
+CCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCA
+ACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA
+CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACC
+AGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAG
+AACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTC
+CTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGT
+AGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCA
+CCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG
+AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCAC
+CGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCG
+TACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCA
+ATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCT
+ATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTA
+TCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC
+CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCAC
+ATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAA
+TATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTC
+CTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCC
+CCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaa
+aaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc
+ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGT
+CAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGC
+GCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCA
+CCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTC
+CTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACAT
+CTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA
+TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGAC
+GAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTA
+CTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA
+TACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTT
+GACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTAC
+ATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA
+CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGA
+CCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG
+TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAG
+GGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTG
+TAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAAC
+ACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA
+TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATA
+TTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAA
+AAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTC
+ATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTC
+TATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGA
+CTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT
+AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCT
+TAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCA
+TTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTT
+ATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCC
+TAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTA
+GTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT
+ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTG
+GAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATC
+ATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTT
+AATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACA
+ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC
+CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA
+GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT
+AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA
+GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC
+GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT
+CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC
+ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC
+CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA
+CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA
+TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC
+TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT
+TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC
+TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT
+CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT
+TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA
+GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA
+AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC
+CTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACA
+TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC
+CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT
+ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA
+CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATC
+CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC
+CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT
+ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA
+GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT
+ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG
+CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT
+ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT
+ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA
+ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC
+TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC
+AGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAA
+CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC
+CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC
+CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC
+TATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG
+AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG
+GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC
+ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC
+TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT
+CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT
+AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT
+TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA
+CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC
+ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC
+TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA
+GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT
+AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA
+TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA
+AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
+ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC
+TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT
+GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG
+ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA
+CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC
+ACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT
+ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTT
+TAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTT
+ATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAA
+CAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA
+GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACA
+CTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACC
+ACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATC
+CATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCA
+TGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACC
+CAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT
+ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCAC
+TGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTA
+CTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATT
+CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA
+TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA
+GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG
+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA
+ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA
+GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA
+AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG
+CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA
+CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC
+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT
+CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA
+CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT
+ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG
+ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC
+TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG
+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA
+ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC
+TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC
+CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA
+AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC
+ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT
+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA
+ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT
+TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC
+CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC
+TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC
+TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT
+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC
+CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT
+TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG
+CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT
+ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA
+CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA
+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA
+ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA
+AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA
+TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA
+GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT
+CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA
+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG
+ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT
+CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT
+CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA
+GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA
+CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA
+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC
+CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT
+CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT
+GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC
+GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA
+CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT
+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC
+GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT
+CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT
+TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC
+GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT
+CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC
+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA
+GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG
+CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC
+TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA
+CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC
+TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA
+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG
+GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA
+GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG
+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC
+ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA
+CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT
+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC
+TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT
+AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC
+AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG
+ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT
+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC
+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC
+CTTAAATAAGACATCACGATG
diff -r 000000000000 -r 2975b29bcaa1 test-data/genome.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta.fai	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,1 @@
+chrM	16571	6	50	51
diff -r 000000000000 -r 2975b29bcaa1 test-data/normal.bam
Binary file test-data/normal.bam has changed
diff -r 000000000000 -r 2975b29bcaa1 test-data/passed_variants_paired.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/passed_variants_paired.vcf	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,92 @@
+##fileformat=VCFv4.1
+##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
+##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
+##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
+##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">
+##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">
+##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
+##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
+##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
+##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
+##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
+##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
+##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
+##FILTER=<ID=Bias,Description="Strand Bias">
+##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
+##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">
+##FILTER=<ID=d5,Description="Total Depth < 5">
+##FILTER=<ID=v3,Description="Var Depth < 3">
+##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
+##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">
+##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
+##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
+##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
+##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
+##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
+##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">
+##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">
+##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">
+##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
+##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
+##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
+##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
+##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
+##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
+##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
+##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
+##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
+##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
+##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
+##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
+##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
+##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Tumor	Normal
+chrM	150	.	T	C	121	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:40.5:1:1:0:60:4:1:0:1.5	1/1:9:9:4,5:0,0:0,9:1:0,2:29.8:1:38.4:1:1:0:60:18:1:0.1111:1.8
+chrM	195	.	C	T	120	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:40:0:1:0:60:2:1:0:2	1/1:9:9:3,6:0,0:0,9:1:0,2:21.9:1:37.9:1:1:0:60:18:1:0:1.8
+chrM	302	.	AC	A	85	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6
+chrM	410	.	A	T	149	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:36.7:1:1:0:60:6:1:0.3333:2.3	1/1:18:18:12,6:0,0:0,18:1:0,2:19.7:1:35.9:1:1:0:60:17:1:0.0556:1.9
+chrM	464	.	C	T	193	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=Inf;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1	1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2
+chrM	491	.	T	C	228	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=Inf;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7	1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7
+chrM	1735	.	C	T	140	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:1,2:0,0:0,3:1:0,2:46.7:1:40.3:1:1:0:60:6:1:0:1	1/1:14:14:6,8:0,0:0,14:1:0,2:26:1:37:1:1:0:60:28:1:0:1.1
+chrM	2354	.	C	T	135	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:36.5:1:1:0:60:6:1:0.3333:1	1/1:11:11:8,3:0,0:0,11:1:0,2:23.1:1:39.1:1:1:0:60:22:1:0.0909:1.3
+chrM	2485	.	C	T	123	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53.3:6:1:0:1	1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40.2:5.5:1:0:1.2
+chrM	3012	.	G	A	99	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58.2:12:1:0:1.2
+chrM	5581	.	C	T	133	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:33.6:24:1:0.0833:1
+chrM	8702	.	G	A	126	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:34:1:1:0:60:4:1:0:1.5	1/1:11:11:6,5:0,0:0,11:1:0,2:25.2:1:36.7:1:1:0:51:22:1:0:1
+chrM	9378	.	G	A	110	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1	1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44.3:8:1:0.1111:1.2
+chrM	11018	.	C	T	84	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51.2:10:1:0:1.2
+chrM	11252	.	A	G	150	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:1,4:0,0:0,5:1:0,2:26.2:1:37.4:1:1:0:60:10:1:0.2:1.2	1/1:17:17:9,8:0,0:0,17:1:0,2:27.8:1:36.9:1:1:0:60:34:1:0.0588:1.2
+chrM	11464	.	T	A	32	PASS	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1	0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2
+chrM	11723	.	C	T	144	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50.4:32:1:0:1
+chrM	12613	.	A	G	106	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3
+chrM	12706	.	T	C	97	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:40:0:1:0:60:2:1:0:1	1/1:6:6:4,2:0,0:0,6:1:0,2:28.7:1:37.7:1:1:0:60:12:1:0:1.3
+chrM	12851	.	G	A	141	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:22.5:1:36.5:1:1:0:60:8:1:0:1	1/1:14:14:7,7:0,0:0,14:1:0,2:26.2:1:37.2:1:1:0:60:28:1:0:1.1
+chrM	13709	.	G	A	103	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1	1/1:7:7:3,4:0,0:0,7:1:0,2:22.3:1:36.7:1:1:0:60:14:1:0:1
+chrM	14213	.	C	T	130	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58.1:22:1:0:1.2
+chrM	14581	.	G	A	141	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:43.6:10:1:0:1	1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56.3:14:1:0.0667:1
+chrM	14794	.	A	G	37	PASS	STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1	0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0
+chrM	14906	.	A	G	177	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:9:9:5,4:0,0:0,9:1:0,2:28.8:1:34.1:1:1:0:60:8:1:0.1111:2.1	1/1:33:33:15,18:0,0:0,33:1:0,2:22.5:1:35.2:1:1:0:60:66:1:0.0606:1.8
+chrM	14928	.	A	G	181	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=Inf;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1	1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8
+chrM	15302	.	A	G	128	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:38:1:1:0:60:4:1:0:1	1/1:11:11:4,7:0,0:0,11:1:0,2:31.2:1:37.1:1:1:0:60:22:1:0:1.2
+chrM	15453	.	C	A	83	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1
+chrM	16070	.	C	T	107	PASS	STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7
+chrM	16127	.	T	C	85	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5	1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2
+chrM	16146	.	G	A	106	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGGTACCATAAATACTT;RSEQ=ACCACCTGTAGTACATAAAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5	1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9
+chrM	16184	.	CC	A	121	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42308;SOR=0.2582;LSEQ=AAAACCCAACCCACATCAAA;RSEQ=CCCCCCCCCCATGCTTACAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:1,0:0,0:0,1:0.5:0,0:27:0:39:0:1:0:60:2:1:0:4	1/1:11:9:7,2:0,0:0,9:0.8182:0,2:28.2:1:38.2:1:1:0:60:18:0.9:0.1818:4.6
+chrM	16191	.	C	T	124	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33.5:1:1:0:60:4:1:0:5.5	1/1:12:12:7,5:0,0:0,12:1:0,2:29.6:1:34.7:1:1:0:60:11:1:0.0833:5.2
+chrM	16224	.	CT	TC	159	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.12566;LSEQ=AAGCAAGTACAGCAATCAAC;RSEQ=TCAACTATCACACATCAACT	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5	1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2
+chrM	16263	.	C	T	158	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3	1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5
+chrM	16322	.	T	C	125	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5	1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5
+chrM	16521	.	C	T	113	PASS	STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1	1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1
diff -r 000000000000 -r 2975b29bcaa1 test-data/passed_variants_single.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/passed_variants_single.vcf	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,89 @@
+##fileformat=VCFv4.1
+##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
+##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
+##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">
+##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">
+##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
+##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
+##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
+##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
+##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
+##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
+##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
+##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
+##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
+##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
+##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
+##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">
+##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
+##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
+##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
+##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">
+##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">
+##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don't work">
+##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don't match">
+##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">
+##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">
+##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">
+##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">
+##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">
+##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
+##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">
+##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
+##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
+##FILTER=<ID=Bias,Description="Strand Bias">
+##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
+##FILTER=<ID=d3,Description="Total Depth < 3">
+##FILTER=<ID=v2,Description="Var Depth < 2">
+##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
+##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">
+##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
+##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">
+##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">
+##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp">
+##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)">
+##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
+##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
+chrM	150	.	T	C	40	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:2;PMEAN=35;PSTD=1;QUAL=40.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:0,2
+chrM	410	.	A	T	58	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=3:0;PMEAN=23.3;PSTD=1;QUAL=36.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;NM=2.3;HICNT=3;HICOV=3;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:3,0
+chrM	464	.	C	T	108	PASS	SAMPLE=Sample;TYPE=SNV;DP=8;VD=8;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=6:2;PMEAN=22.8;PSTD=1;QUAL=36.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=16;HIAF=1.0000;ADJAF=0;SHIFT3=2;MSI=3;MSILEN=1;NM=2.1;HICNT=8;HICOV=8;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:8:8:0,8:1:0,0:6,2
+chrM	491	.	T	C	127	PASS	SAMPLE=Sample;TYPE=SNV;DP=10;VD=10;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=8:2;PMEAN=28.3;PSTD=1;QUAL=38.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=20;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.7;HICNT=10;HICOV=10;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:10:10:0,10:1:0,0:8,2
+chrM	681	.	C	T	30	PASS	SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=70:52;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.34287;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:124:2:122,2:0.0161:70,52:1,1
+chrM	692	.	T	C	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=73:49;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=1.48485;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:124:2:122,2:0.0161:73,49:1,1
+chrM	737	.	A	G	30	PASS	SAMPLE=Sample;TYPE=SNV;DP=106;VD=2;AF=0.0189;BIAS=2:2;REFBIAS=42:61;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.44707329426235;MQ=60;SN=4;HIAF=0.0202;ADJAF=0.0094;SHIFT3=1;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=99;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:106:2:103,2:0.0189:42,61:1,1
+chrM	1735	.	C	T	63	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:2;PMEAN=46.7;PSTD=1;QUAL=40.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=3;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:1,2
+chrM	2354	.	C	T	57	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=18.3;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=4;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:2,1
+chrM	2485	.	C	T	59	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=17.7;PSTD=1;QUAL=37.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=53.3;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:2,1
+chrM	6720	.	T	C	75	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=56;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	8702	.	G	A	34	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=46;PSTD=1;QUAL=34;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	9378	.	G	A	57	PASS	SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:3;PMEAN=20.3;PSTD=1;QUAL=36;QSTD=1;SBF=1;ODDRATIO=0;MQ=46;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:3:3:0,3:1:0,0:0,3
+chrM	9541	.	C	T	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=48.5;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	10874	.	C	T	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=30;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=5;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	11198	.	C	A	31	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=2;AF=0.2222;BIAS=2:2;REFBIAS=3:4;VARBIAS=1:1;PMEAN=31.5;PSTD=1;QUAL=31.5;QSTD=1;SBF=1;ODDRATIO=1.29098889749548;MQ=60;SN=4;HIAF=0.2222;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=2;NM=1.5;HICNT=2;HICOV=9;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:9:2:7,2:0.2222:3,4:1,1
+chrM	11252	.	A	G	86	PASS	SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:4;PMEAN=26.2;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=10;HIAF=1.0000;ADJAF=0.2;SHIFT3=0;MSI=2;MSILEN=1;NM=1.2;HICNT=5;HICOV=5;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:5:5:0,5:1:0,0:1,4
+chrM	11464	.	T	A	32	PASS	SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=25.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:6:2:4,2:0.3333:2,2:1,1
+chrM	12851	.	G	A	73	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=22.5;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	13709	.	G	A	32	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	14581	.	G	A	86	PASS	SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:5:5:0,5:1:0,0:3,2
+chrM	14794	.	A	G	37	PASS	SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	0/1:6:2:4,2:0.3333:2,2:1,1
+chrM	14906	.	A	G	108	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:9:9:0,9:1:0,0:5,4
+chrM	14928	.	A	G	122	PASS	SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:9:9:0,9:1:0,0:5,4
+chrM	15302	.	A	G	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16263	.	C	T	68	PASS	SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:4:4:0,4:1:0,0:2,2
+chrM	16322	.	T	C	33	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
+chrM	16521	.	C	T	38	PASS	SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0	GT:DP:VD:AD:AF:RD:ALD	1/1:2:2:0,2:1:0,0:1,1
diff -r 000000000000 -r 2975b29bcaa1 test-data/tumor.bam
Binary file test-data/tumor.bam has changed
diff -r 000000000000 -r 2975b29bcaa1 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 2975b29bcaa1 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc"/>
+    </table>
+</tables>
diff -r 000000000000 -r 2975b29bcaa1 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of SAMTools indexed FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 2975b29bcaa1 vardict.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vardict.xml	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,176 @@
+<tool id="vardict_java" name="VarDict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>calls SNVs and indels for tumor-normal pairs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
+        <requirement type="package" version="5.0.1">gawk</requirement>
+        <requirement type="package" version="1.10">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $select_mode.mode == "paired"
+            ln -s '$select_mode.normal' ./normal.bam &&
+            ln -s '$select_mode.normal.metadata.bam_index' ./normal.bam.bai &&
+        #end if
+        ln -s '$select_mode.tumor' ./tumor.bam &&
+        ln -s '$select_mode.tumor.metadata.bam_index' ./tumor.bam.bai &&
+
+        ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
+        #if $reference_source.reference_source_selector == "history":
+            ln -s '$reference_source.ref_file' ./ref.fa &&
+            samtools faidx ./ref.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for vardict' >&2 &&
+        #else if $reference_source.reference_source_selector == "cached"
+            ln -s '$reference_source.ref_file.fields.path' ./ref.fa &&
+            ln -s '${reference_source.ref_file.fields.path}.fai' ./ref.fa.fai &&
+        #end if
+
+        ## build BED file from chromosome list
+        #if $interval_file:
+            grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
+        #else
+            ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
+        #end if
+        awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed &&
+
+        vardict-java
+        #if $select_mode.mode == "paired"
+            -b "./tumor.bam|./normal.bam"
+            -N 'Tumor'
+        #else
+            -b "./tumor.bam"
+            -N 'Sample'
+        #end if
+        -G ./ref.fa
+        -z
+        -th \${GALAXY_SLOTS:-1}
+
+        -f '$advancedsettings.f'
+        -k '$advancedsettings.k'
+        -r '$advancedsettings.r'
+        -B '$advancedsettings.B'
+        -Q '$advancedsettings.Q'
+        -q '$advancedsettings.q'
+        -m '$advancedsettings.m'
+        -T '$advancedsettings.T'
+        -X '$advancedsettings.X'
+        -P '$advancedsettings.P'
+        -o '$advancedsettings.o'
+        -O '$advancedsettings.O'
+        -V '$advancedsettings.V'
+
+        ## construct VFC table
+        -c 1 -S 2 -E 3 -g 4
+        ./regions.bed
+
+        ## postprocessing
+        #if $select_mode.mode == "paired"
+            | testsomatic.R
+            | var2vcf_paired.pl
+            -N 'Tumor|Normal'
+        #else
+            | teststrandbias.R
+            | var2vcf_valid.pl
+            -N 'Sample'
+            -E
+        #end if
+         -f '$advancedsettings.f'
+
+        > '$all_variants' &&
+
+        ## Filter for PASS variants
+        awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' '$all_variants' > '$passed_variants'
+    ]]></command>
+    <inputs>
+        <conditional name="select_mode">
+            <param name="mode" type="select" label="Choose run mode">
+                <option value="single">Single sample mode</option>
+                <option value="paired" selected="True">Paired variant calling</option>
+            </param>
+            <when value="single">
+                <expand macro="input_default" />
+            </when>
+            <when value="paired">
+                <param name="normal" type="data" format="bam" label="Normal file" />
+                <expand macro="input_default" />
+            </when>
+        </conditional>
+        <section name="advancedsettings" title="Advanced Settings" expanded="False">
+            <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" />
+            <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" />
+            <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" />
+            <param argument="-B" type="integer" min="0" value="2" label="Minimum number of reads for determining strand bias" />
+            <param argument="-Q" type="integer" min="0" value="1" label="Minimum mapping quality for reads to be considered" />
+            <param argument="-m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" />
+            <param argument="-T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" />
+            <param argument="-X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />
+            <param argument="-P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />
+            <param argument="-q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />
+            <param argument="-o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />
+            <param argument="-O" type="float" min="0" value="0" label="Minimum average mapping quality" />
+            <param argument="-V" type="float" min="0.0" max="1.0" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />
+        </section>
+        <expand macro="ref_select" />
+    </inputs>
+    <outputs>
+        <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />
+        <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="paired" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <output name="all_variants" file="all_variants_paired.vcf" />
+            <output name="passed_variants" file="passed_variants_paired.vcf" />
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="paired" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="test_buildid"/>
+            </conditional>
+            <output name="all_variants" file="all_variants_paired.vcf" />
+            <output name="passed_variants" file="passed_variants_paired.vcf" />
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="single" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="test_buildid"/>
+            </conditional>
+            <output name="all_variants" file="all_variants_single.vcf" />
+            <output name="passed_variants" file="passed_variants_single.vcf" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+VarDict
+=======
+
+VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files.
+VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments,
+rescue of long indels by realigning bwa soft clipped reads and better scalability than many other Java based variant callers.
+
+For more information see the VarDict documentation_.
+
+.. _documentation: https://github.com/AstraZeneca-NGS/VarDictJava
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkw227</citation>
+    </citations>
+</tool>