Mercurial > repos > iuc > vcfanno

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jan 21 10:33:49 2021 +0000
@@ -0,0 +1,69 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">vcfanno</requirement>
+            <requirement type="package">tabix</requirement>
+            <requirement type="package">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>vcfanno --help</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{vcfanno,
+              author = {Brent S. Pedersen},
+              title = {vcfanno},
+              year = 2016,
+              url = {https://github.com/brentp/vcfanno},
+              urldate = {2020-12-03}
+            }</citation>
+            <citation type="doi">10.1186/s13059-016-0973-5</citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">vcfanno</xref>
+        </xrefs>
+    </xml>
+
+    <!--
+        Inputs
+    -->
+    <macro name = "ops">
+        <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option>
+        <option value="concat">concat - comma delimited list of output</option>
+        <option value="count">count - count the number of overlaps</option>
+        <option value="div2">div2 - given two values a and b, return a / b</option>
+        <option value="first">first - take only the first value</option>
+        <option value="flag">flag - presense/absence via VCF flag</option>
+        <option value="max">max (numbers only)</option>
+        <option value="mean">mean (numbers only)</option>
+        <option value="min">min (numbers only)</option>
+        <option value="sum">sum (numbers only)</option>
+        <option value="uniq">uniq - comma-delimited list of uniq values</option>
+        <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option>
+        <yield/>
+    </macro>
+
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+*vcfanno* allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.
+
+ - For VCF, values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns.
+
+ - For BED, values are pulled from (1-based) column number.
+
+ - For BAM, depth (count), "mapq" and "seq" are currently supported.
+ ]]></token>
+    <token name="@REFERENCES@"><![CDATA[
+More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_.
+    ]]></token>
+</macros>
Binary file test-data/ex.bam has changed
Binary file test-data/ex.bam.bai has changed
Binary file test-data/exac.vcf.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitcons.bed	Thu Jan 21 10:33:49 2021 +0000
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Binary file test-data/query.vcf.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfanno_result.vcf	Thu Jan 21 10:33:49 2021 +0000
@@ -0,0 +1,487 @@
+##fileformat=VCFv4.1
+##contig=<ID=1>
+##contig=<ID=10>
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+##contig=<ID=MT>
+##contig=<ID=X>
+##contig=<ID=Y>
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AC_AFR,Number=A,Type=Integer,Description="African/African American Allele Counts (from input_0.vcf.gz)">
+##INFO=<ID=AC_AMR,Number=A,Type=Integer,Description="American Allele Counts (from input_0.vcf.gz)">
+##INFO=<ID=AC_EAS,Number=A,Type=Integer,Description="East Asian Allele Counts (from input_0.vcf.gz)">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=ICIEND,Number=2,Type=Integer,Description="CIEND">
+##INFO=<ID=ICIPOS,Number=2,Type=Integer,Description="CIPOS">
+##INFO=<ID=ID,Number=1,Type=String,Description="calculated by first of overlapping values in field ID from input_0.vcf.gz">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
+##INFO=<ID=OLD_VARIANT,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=coverage,Number=1,Type=Float,Description="calculated by sum of overlapping values in field coverage from input_1.bam">
+##INFO=<ID=lua_end,Number=1,Type=String,Description="calculated by first of overlapping values in column 4 from input_2.bed.gz">
+##INFO=<ID=lua_len,Number=1,Type=String,Description="calculated by first of overlapping values in column 4 from input_2.bed.gz">
+##INFO=<ID=lua_loc,Number=1,Type=String,Description="calculated by first of overlapping values in column 4 from input_2.bed.gz">
+##INFO=<ID=lua_mean,Number=1,Type=String,Description="calculated by first of overlapping values in column 4 from input_2.bed.gz">
+##INFO=<ID=lua_start,Number=1,Type=String,Description="calculated by first of overlapping values in column 4 from input_2.bed.gz">
+##INFO=<ID=mapq,Number=1,Type=Float,Description="calculated by mean of overlapping values in field mapq from input_1.bam">
+##INFO=<ID=xdp2,Number=2,Type=Integer,Description="calculated by coverage from input_1.bam values are numbers of forward,reverse reads">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##fileDate=20140830
+##source=freeBayes v0.9.14
+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
+##phasing=none
+##commandline="/mnt/thor_pool1/user_data/cc2qe/code/speedseq/bin/freebayes -f /shared/genomes/b37/full/human_g1k_v37.fasta --region MT:12136..12498 bam/NA12877_S1/NA12877_S1.bam bam/NA12878_S1/NA12878_S1.bam bam/NA12879_S1/NA12879_S1.bam bam/NA12880_S1/NA12880_S1.bam bam/NA12881_S1/NA12881_S1.bam bam/NA12882_S1/NA12882_S1.bam bam/NA12883_S1/NA12883_S1.bam bam/NA12884_S1/NA12884_S1.bam bam/NA12885_S1/NA12885_S1.bam bam/NA12886_S1/NA12886_S1.bam bam/NA12887_S1/NA12887_S1.bam bam/NA12888_S1/NA12888_S1.bam bam/NA12889_S1/NA12889_S1.bam bam/NA12890_S1/NA12890_S1.bam bam/NA12891_S1/NA12891_S1.bam bam/NA12892_S1/NA12892_S1.bam bam/NA12893_S1/NA12893_S1.bam"
+##VEP=v76 cache=/shared/external_bin/ensembl-tools-release-76/cache/homo_sapiens/76_GRCh37 db=.
+##SnpEffVersion="3.6c (build 2014-05-20), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  GRCh37.75 "
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12889	NA12890	NA12877
+1	10492	.	C	T	3055.1	.	AB=0.188084;ABP=726.385;AC=9;AF=0.264706;AN=34;AO=167;CIGAR=1X;TYPE=snp;mapq=55.5;coverage=12;xdp2=4,8	GT:DP:RO:QR:AO:QA:GL	0/0:117:117:3837:0:0:0,-10,-10	0/0:113:113:3758:0:0:0,-10,-10	0/0:132:132:4396:0:0:0,-10,-10
+1	10583	.	G	A	1071.5	.	AB=0.191964;ABP=372.238;AC=8;AF=0.235294;AN=34;AO=104;CIGAR=1X;TYPE=snp;mapq=52.6667;coverage=3;xdp2=1,2	GT:DP:RO:QR:AO:QA:GL	0/1:61:40:1252:20:580:-10,0,-10	0/0:57:51:1697:6:175:-6.44272,0,-10	0/0:64:56:1738:7:207:-8.6143,0,-10
+1	10616	.	CCGCCGTTGCAAAGGCGCGCCG	C	580.2	.	AB=0.4375;ABP=3.55317;AC=31;AF=0.911765;AN=34;AO=54;CIGAR=1M21D1M;TYPE=del;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:35:-3.325,-0.60206,0	1/1:5:0:0:4:106:-9.744,-1.20412,0	1/1:9:0:0:9:208:-10,-2.70927,0
+1	10623	.	TGCAAAGGC	CGCAAAG	580.2	.	AB=0.375;ABP=5.18177;AC=3;AF=0.0882353;AN=34;AO=10;CIGAR=7M1X6M2D7M;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	./.:2:0:0:0:0:-3.325,-3.325,-3.325	./.:5:0:0:0:0:-9.744,-9.744,-9.744	./.:9:0:0:0:0:-10,-10,-10
+1	10654	.	G	C	19.3	.	AB=0.26087;ABP=14.4341;AC=2;AF=0.0588235;AN=34;AO=14;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:10:10:273:0:0:0,-3.0103,-10	0/0:10:10:338:0:0:0,-3.0103,-10	0/0:20:19:610:1:7:0,-4.01957,-10
+1	10664	.	C	G	125.0	.	AB=0.291667;ABP=30.1537;AC=5;AF=0.147059;AN=34;AO=32;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:10:10:241:0:0:0,-3.0103,-10	0/0:9:9:308:0:0:0,-2.70927,-10	0/0:20:19:530:1:31:0,-1.61957,-10
+1	10665	.	C	G	717.5	.	AB=0.406639;ABP=21.2561;AC=17;AF=0.5;AN=34;AO=98;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/1:10:6:136:4:114:-9.85692,0,-10	0/1:9:4:139:5:139:-10,0,-10	0/1:20:13:390:7:147:-10,0,-10
+1	10671	.	G	C	215.9	.	AB=0.304878;ABP=30.1272;AC=7;AF=0.205882;AN=34;AO=33;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:9:9:254:0:0:0,-2.70927,-10	0/0:6:6:163:0:0:0,-1.80618,-10	0/1:12:11:273:1:39:-1.36682,0,-10
+1	10683	.	G	C	244.6	.	AB=0.3125;ABP=17.6677;AC=4;AF=0.117647;AN=34;AO=20;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:8:8:264:0:0:0,-2.40824,-10	0/0:8:8:220:0:0:0,-2.40824,-10	0/0:11:11:324:0:0:0,-3.31133,-10
+1	10693	.	C	G	281.7	.	AB=0.343284;ABP=17.3031;AC=6;AF=0.176471;AN=34;AO=31;CIGAR=1X;TYPE=snp;mapq=21;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:8:8:241:0:0:0,-2.40824,-10	0/0:8:8:236:0:0:0,-2.40824,-10	0/0:11:11:359:0:0:0,-3.31133,-10
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+1	62578	.	G	A	177.6	.	AB=1;ABP=31.2394;AC=4;AF=0.133333;AN=30;AO=25;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:137:137:5182:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:36:35:1324:1:37:0,-5.58078,-10
+1	62777	.	A	T	4344.6	.	AB=0.344828;ABP=69.7269;AC=16;AF=0.470588;AN=34;AO=147;CIGAR=1X;TYPE=snp;mapq=28.1429;coverage=7;xdp2=2,5	GT:DP:RO:QR:AO:QA:GL	0/0:116:116:4181:0:0:0,-10,-10	1/1:12:0:0:12:465:-10,-3.61236,0	0/1:32:25:873:7:239:-10,0,-10
+1	63239	.	C	T	78.9	.	AB=1;ABP=20.3821;AC=3;AF=0.115385;AN=26;AO=16;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:70:69:2539:1:34:0,-10,-10	.:.:.:.:.:.:.	0/0:30:30:1134:0:0:0,-9.0309,-10
+1	63268	.	T	C	331.4	.	AB=1;ABP=55.1256;AC=7;AF=0.233333;AN=30;AO=39;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:76:70:2639:6:199:-3.70307,0,-10	.:.:.:.:.:.:.	0/0:25:24:904:1:17:0,-4.42781,-10
+1	63336	.	C	T	3933.0	.	AB=0.549356;ABP=7.94038;AC=7;AF=0.205882;AN=34;AO=128;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:70:49:1805:21:792:-10,0,-10	0/0:6:6:243:0:0:0,-1.80618,-10	0/1:25:8:314:17:627:-10,0,-10
+1	63495	.	C	T	879.9	.	AB=0.481481;ABP=3.25157;AC=8;AF=0.235294;AN=34;AO=39;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:68:68:2525:0:0:0,-10,-10	0/0:3:3:109:0:0:0,-0.90309,-10	0/0:17:17:633:0:0:0,-5.11751,-10
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+1	63527	.	T	C	636.3	.	AB=0.435294;ABP=6.10145;AC=10;AF=0.333333;AN=30;AO=46;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:63:58:2091:5:176:-4.07399,0,-10	.:.:.:.:.:.:.	0/0:14:13:475:1:35:-0.431708,0,-10
+1	63671	.	G	A	439.4	.	AB=0.204545;ABP=69.7337;AC=1;AF=0.0294118;AN=34;AO=18;CIGAR=1X;TYPE=snp;mapq=12.25;coverage=4;xdp2=0,4	GT:DP:RO:QR:AO:QA:GL	0/1:88:69:2494:18:673:-10,0,-10	0/0:23:23:859:0:0:0,-6.92369,-10	0/0:43:43:1556:0:0:0,-10,-10
+1	63697	.	T	C	3900.2	.	AB=0.397727;ABP=26.9952;AC=11;AF=0.323529;AN=34;AO=132;CIGAR=1X;TYPE=snp;mapq=25;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/1:64:56:2024:8:295:-10,0,-10	0/0:17:17:620:0:0:0,-5.11751,-10	0/0:42:42:1551:0:0:0,-10,-10
+1	63735	.	CCTA	C	2709.8	.	AB=0.603448;ABP=19.184;AC=11;AF=0.323529;AN=34;AO=153;CIGAR=1M3D4M;TYPE=del;mapq=25;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	1/1:50:2:65:48:1228:-10,-5.78836,0	0/0:7:7:233:0:0:0,-2.10721,-10	0/1:27:10:342:17:358:-10,0,-10
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+1	64548	.	ACTAG	CCTAA	1161.6	.	AB=0.396947;ABP=15.0943;AC=13;AF=0.382353;AN=34;AO=52;CIGAR=1X3M1X;TYPE=complex;mapq=40;coverage=2;xdp2=2,0	GT:DP:RO:QR:AO:QA:GL	0/0:18:18:639:0:0:0,-5.41854,-10	0/1:5:2:70:3:94:-8.26818,0,-6.14485	0/1:15:11:385:4:156:-10,0,-10
+1	64613	.	T	A	1408.7	.	AB=0.224852;ABP=225.271;AC=9;AF=0.264706;AN=34;AO=82;CIGAR=1X;TYPE=snp;mapq=46;coverage=5;xdp2=3,2	GT:DP:RO:QR:AO:QA:GL	0/1:47:41:1511:6:218:-10,0,-10	0/1:19:9:340:10:335:-10,0,-10	0/1:42:30:1063:12:417:-10,0,-10
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+1	64927	.	G	T	310.2	.	AB=0.314815;ABP=19.0953;AC=3;AF=0.0882353;AN=34;AO=27;CIGAR=1X;TYPE=snp;mapq=36.5;coverage=2;xdp2=0,2	GT:DP:RO:QR:AO:QA:GL	0/0:63:61:2264:2:78:0,-8.26419,-10	0/1:16:8:274:8:309:-10,0,-10	0/0:35:33:1193:2:80:0,-0.161533,-10
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+1	66221	.	A	AT	968.3	.	AB=0.411215;ABP=10.3365;AC=12;AF=0.352941;AN=34;AO=47;CIGAR=1M1I2M;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	0/0:5:5:196:0:0:0,-1.50515,-10	0/1:4:2:81:2:69:-6.12903,0,-7.26903	0/1:24:14:537:9:300:-10,0,-10
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+1	66300	.	A	AT	88.4	.	AB=0.16129;ABP=33.9012;AC=1;AF=0.0833333;AN=12;AO=5;CIGAR=2M1I1M;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	.:.:.:.:.:.:.	.:.:.:.:.:.:.	0/1:21:16:612:3:121:-8.16175,0,-10
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+1	66375	.	ATAA	TAT	1265.4	.	AB=0.217949;ABP=56.9074;AC=4;AF=0.285714;AN=14;AO=17;CIGAR=3M1D2M1X1M;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	.:.:.:.:.:.:.	.:.:.:.:.:.:.	./.:33:0:0:7:264:-10,-10,-10
+1	66376	.	TA	T	1265.4	.	AB=0.223684;ABP=53.4113;AC=2;AF=0.142857;AN=14;AO=17;CIGAR=5M1D2M;TYPE=del	GT:DP:RO:QR:AO:QA:GL	.:.:.:.:.:.:.	.:.:.:.:.:.:.	./1:33:0:0:9:361:-10,-10,-10
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+1	83574	.	G	T	280.6	.	AB=0.285714;ABP=19.7617;AC=1;AF=0.0416667;AN=24;AO=12;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:42:30:1120:12:433:-10,0,-10	.:.:.:.:.:.:.	0/0:7:7:266:0:0:0,-2.10721,-10
+1	83786	.	T	TA	75.9	.	AB=0.413043;ABP=6.03148;AC=5;AF=0.178571;AN=28;AO=33;CIGAR=1M1I9M;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	0/0:74:73:2710:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:22:20:728:2:6:0,-3.68905,-10
+1	83819	.	A	AAGAAAG	342.3	.	AB=0.394366;ABP=9.89173;AC=7;AF=0.25;AN=28;AO=29;CIGAR=5M6I9M;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	0/0:64:61:2187:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:19:19:675:0:0:0,-5.71957,-10
+1	83829	.	G	GAGAA	469.4	.	AB=0.363636;ABP=8.34028;AC=6;AF=0.230769;AN=26;AO=14;CIGAR=1M4I45M;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	0/.:37:26:979:0:0:-10,-10,-10	.:.:.:.:.:.:.	0/0:10:10:343:0:0:0,-3.0103,-10
+1	83829	.	GAGAA	G	469.4	.	AB=0;ABP=0;AC=2;AF=0.0769231;AN=26;AO=16;CIGAR=1M4D41M;TYPE=del	GT:DP:RO:QR:AO:QA:GL	0/.:37:26:979:0:0:-10,-10,-10	.:.:.:.:.:.:.	0/0:10:10:343:0:0:0,-3.0103,-10
+1	83854	.	AGAAAGAAAGAAAGAAAG	GAGAAAGAAAGAAAGAAGA	469.4	.	AB=0.189189;ABP=34.0565;AC=1;AF=0.0384615;AN=26;AO=7;CIGAR=25M1I16M2X3M;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	0/1:37:26:979:7:184:-10,0,-10	.:.:.:.:.:.:.	0/0:10:10:343:0:0:0,-3.0103,-10
+1	83878	.	AAGAAAGAAAG	A	10.1	.	AB=0.170732;ABP=41.6201;AC=3;AF=0.09375;AN=32;AO=18;CIGAR=1M10D1M;TYPE=del	GT:DP:RO:QR:AO:QA:GL	0/0:90:87:3239:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:26:24:897:1:40:0,-2.36281,-10
+1	83895	.	GAGAA	G	1472.9	.	AB=0.609756;ABP=11.5903;AC=6;AF=0.230769;AN=26;AO=50;CIGAR=1M4D13M;TYPE=del	GT:DP:RO:QR:AO:QA:GL	0/1:82:25:926:50:1839:-10,0,-10	.:.:.:.:.:.:.	0/0:30:29:1089:0:0:0,-8.72987,-10
+1	83978	.	G	A	36.4	.	AB=0.25;ABP=13.8677;AC=1;AF=0.0384615;AN=26;AO=5;CIGAR=1X;TYPE=snp;mapq=35;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:99:99:3560:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:27:27:956:0:0:0,-8.12781,-10
+1	83998	.	G	A	2231.2	.	AB=0.252964;ABP=137.118;AC=3;AF=0.115385;AN=26;AO=64;CIGAR=1X1M;TYPE=snp;mapq=35;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/1:99:66:2388:24:845:-10,0,-10	.:.:.:.:.:.:.	0/.:20:6:218:5:149:-10,-10,-10
+1	83998	.	G	GAAAA	2231.2	.	AB=0.258621;ABP=120.42;AC=4;AF=0.153846;AN=26;AO=60;CIGAR=1M4I1M;TYPE=ins;mapq=35;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/.:99:66:2388:9:279:-10,-10,-10	.:.:.:.:.:.:.	0/1:20:6:218:9:315:-10,0,-10
+1	84002	.	G	A	2055.1	.	AB=0.278571;ABP=122.255;AC=8;AF=0.285714;AN=28;AO=78;CIGAR=1X;TYPE=snp;mapq=35;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/1:110:95:3465:15:537:-10,0,-10	.:.:.:.:.:.:.	0/1:21:14:501:7:247:-10,0,-10
+1	84026	.	GAA	G	338.3	.	AB=0.758621;ABP=19.8579;AC=7;AF=0.233333;AN=30;AO=31;CIGAR=1M2D1M;TYPE=del;mapq=34.5;coverage=2;xdp2=1,1	GT:DP:RO:QR:AO:QA:GL	0/0:120:119:4285:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:29:27:939:0:0:0,-8.12781,-10
+1	84133	.	A	T	2789.0	.	AB=0.460526;ABP=6.09608;AC=8;AF=0.235294;AN=34;AO=105;CIGAR=1X;TYPE=snp;mapq=29.6667;coverage=3;xdp2=1,2	GT:DP:RO:QR:AO:QA:GL	0/0:91:91:3219:0:0:0,-10,-10	0/0:8:8:310:0:0:0,-2.40824,-10	0/0:43:43:1569:0:0:0,-10,-10
+1	84214	.	AT	A	31.4	.	AB=0.492063;ABP=3.04477;AC=5;AF=0.178571;AN=28;AO=62;CIGAR=1M1D6M;TYPE=del;mapq=27.5;coverage=2;xdp2=0,2	GT:DP:RO:QR:AO:QA:GL	0/0:94:93:3532:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:33:32:1215:1:15:0,-6.91548,-10
+1	84230	.	T	C	851.5	.	AB=0.223958;ABP=130.087;AC=9;AF=0.28125;AN=32;AO=49;CIGAR=1X;TYPE=snp;mapq=15;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:100:100:3771:0:0:0,-10,-10	0/0:1:0:0:1:36:-3.6,-0.30103,0	0/0:32:30:1166:2:74:-0.0925218,0,-10
+1	84307	.	C	A	3840.1	.	AB=0.348432;ABP=60.2782;AC=19;AF=0.558824;AN=34;AO=144;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:112:110:4158:2:77:0,-10,-10	0/1:3:0:0:3:123:-10,-0.90309,0	0/1:34:27:1051:7:253:-10,0,-10
+1	85022	.	G	A	2889.1	.	AB=0.378788;ABP=36.701;AC=8;AF=0.235294;AN=34;AO=100;CIGAR=1X;TYPE=snp;mapq=27;coverage=10;xdp2=6,4	GT:DP:RO:QR:AO:QA:GL	0/0:102:100:3656:0:0:0,-10,-10	0/0:9:9:337:0:0:0,-2.70927,-10	0/0:42:42:1546:0:0:0,-10,-10
+1	85150	.	G	A	100.9	.	AB=1;ABP=29.068;AC=4;AF=0.142857;AN=28;AO=26;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:95:95:3612:0:0:0,-10,-10	0/0:1:0:0:1:35:-3.5,-0.30103,0	0/0:46:46:1763:0:0:0,-10,-10
+1	85200	.	T	C	1.4	.	AB=1;ABP=9.52472;AC=1;AF=0.0454545;AN=22;AO=10;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:91:91:3410:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:34:33:1281:1:35:0,-5.20354,-10
+1	87190	.	G	A	636.0	.	AB=0.349206;ABP=15.4532;AC=1;AF=0.0714286;AN=14;AO=22;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:63:41:1446:22:808:-10,0,-10	.:.:.:.:.:.:.	0/0:34:34:1240:0:0:0,-10,-10
+1	88169	.	C	T	250.5	.	AB=0.203125;ABP=52.0041;AC=1;AF=0.0714286;AN=14;AO=13;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:64:51:1877:13:415:-10,0,-10	.:.:.:.:.:.:.	0/0:23:23:790:0:0:0,-6.92369,-10
+1	88338	.	G	A	610.8	.	AB=0.359375;ABP=14.0034;AC=1;AF=0.0625;AN=16;AO=23;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:64:40:1306:23:797:-10,0,-10	.:.:.:.:.:.:.	0/0:20:20:677:0:0:0,-6.0206,-10
+1	88370	.	G	A	587.5	.	AB=0.366667;ABP=12.2752;AC=1;AF=0.0625;AN=16;AO=22;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:60:38:1266:22:763:-10,0,-10	0/0:1:1:37:0:0:0,-0.30103,-3.7	0/0:21:21:766:0:0:0,-6.32163,-10
+1	89946	.	A	T	487.5	.	AB=0;ABP=0;AC=2;AF=0.142857;AN=14;AO=20;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:82:82:3025:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:32:31:1142:1:17:0,-6.42781,-10
+1	91119	.	C	T	262.4	.	AB=0.264151;ABP=28.6173;AC=1;AF=0.0454545;AN=22;AO=14;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:53:39:1297:14:417:-10,0,-10	0/0:2:2:67:0:0:0,-0.60206,-6.365	0/0:23:23:741:0:0:0,-6.92369,-10
+1	91256	.	A	G	78.3	.	AB=0.209302;ABP=34.5724;AC=4;AF=0.166667;AN=24;AO=14;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:56:53:1754:2:82:0,-5.77826,-10	0/0:2:2:76:0:0:0,-0.60206,-7.22	0/0:10:10:353:0:0:0,-3.0103,-10
+1	91268	.	G	A	125.3	.	AB=0.243902;ABP=26.3669;AC=5;AF=0.208333;AN=24;AO=14;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:48:45:1380:2:81:0,-3.58792,-10	0/0:2:2:74:0:0:0,-0.60206,-7.03	0/0:12:12:361:0:0:0,-3.61236,-10
+1	91336	.	A	T	290.1	.	AB=0.444444;ABP=3.73412;AC=2;AF=0.125;AN=16;AO=12;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:26:15:516:11:382:-10,0,-10	0/1:1:0:0:1:33:-3.3,-0.30103,0	0/0:14:14:465:0:0:0,-4.21442,-10
+1	91475	.	G	A	429.0	.	AB=0.357143;ABP=12.937;AC=9;AF=0.45;AN=20;AO=23;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:38:28:964:10:358:-10,0,-10	.:.:.:.:.:.:.	0/1:4:1:5:3:111:-9.86,-0.10206,0
+1	91486	.	GTACA	CTACG	46.6	.	AB=0.454545;ABP=3.20771;AC=4;AF=0.222222;AN=18;AO=6;CIGAR=1X3M1X;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	0/0:25:23:809:1:38:0,-2.26951,-10	.:.:.:.:.:.:.	0/1:1:0:0:1:39:-3.9,-0.30103,0
+1	91581	.	G	A	542.8	.	AB=0.217391;ABP=18.9659;AC=16;AF=0.8;AN=20;AO=22;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:20:17:579:2:72:-3.17343,0,-10	0/1:1:0:0:1:40:-4,-0.30103,0	1/1:3:0:0:3:104:-9.70667,-0.90309,0
+1	91731	.	G	A	1953.5	.	AB=0.666667;ABP=12.42;AC=17;AF=0.772727;AN=22;AO=68;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:33:12:443:21:714:-10,0,-10	0/1:1:1:39:0:0:0,-0.30103,-3.9	1/1:10:0:0:10:345:-10,-3.0103,0
+1	92481	.	G	A	114.6	.	AB=0.27027;ABP=19.9713;AC=6;AF=0.176471;AN=34;AO=11;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:13:13:430:0:0:0,-3.91339,-10	0/1:4:3:116:1:41:-3.49794,0,-10	0/0:6:6:203:0:0:0,-1.80618,-10
+1	92633	.	C	T	629.6	.	AB=0.857143;ABP=34.0313;AC=2;AF=0.0833333;AN=24;AO=25;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:48:48:1571:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:31:31:1001:0:0:0,-9.33193,-10
+1	92654	.	T	C	65.1	.	AB=0.857143;ABP=18.5208;AC=4;AF=0.125;AN=32;AO=26;CIGAR=1X;TYPE=snp;mapq=10;coverage=2;xdp2=2,0	GT:DP:RO:QR:AO:QA:GL	0/0:56:53:1669:3:62:0,-6.62822,-10	0/1:3:0:0:3:59:-5.50667,-0.90309,0	0/0:32:30:975:1:7:0,-7.20557,-10
+1	92858	.	G	T	807.0	.	AB=0;ABP=0;AC=2;AF=0.125;AN=16;AO=29;CIGAR=1X;TYPE=snp;mapq=31;coverage=1;xdp2=0,1	GT:DP:RO:QR:AO:QA:GL	0/0:74:74:2761:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:28:28:1042:0:0:0,-8.42884,-10
+1	92875	.	T	C	747.8	.	AB=0;ABP=0;AC=2;AF=0.0909091;AN=22;AO=29;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:75:75:2750:0:0:0,-10,-10	.:.:.:.:.:.:.	0/0:30:30:1126:0:0:0,-9.0309,-10
+1	92930	.	G	T	50.1	.	AB=0.225806;ABP=23.254;AC=2;AF=0.0625;AN=32;AO=11;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:43:42:1526:1:29:0,-8.41082,-10	0/0:4:4:152:0:0:0,-1.20412,-10	0/0:23:23:800:0:0:0,-6.92369,-10
+1	93757	.	C	T	61.6	.	AB=0.222222;ABP=15.074;AC=1;AF=0.0714286;AN=14;AO=4;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:18:14:516:4:155:-10,0,-10	.:.:.:.:.:.:.	0/0:7:7:253:0:0:0,-2.10721,-10
+1	94260	.	G	A	57.4	.	AB=0.285714;ABP=8.59409;AC=1;AF=0.0333333;AN=30;AO=5;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:45:45:1548:0:0:0,-10,-10	0/1:14:10:376:4:154:-10,0,-10	0/0:12:12:442:0:0:0,-3.61236,-10
+1	94271	.	C	G	4600.8	.	AB=0.560166;ABP=10.5879;AC=18;AF=0.6;AN=30;AO=165;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:47:34:1165:13:490:-10,0,-10	0/1:14:4:156:10:381:-10,0,-10	0/1:13:10:381:3:104:-8.24964,0,-10
+1	94570	.	T	G	614.0	.	AB=0.328947;ABP=22.325;AC=15;AF=0.441176;AN=34;AO=32;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:14:12:450:2:82:-5.53462,0,-10	0/0:7:6:227:1:29:-1.63789,0,-10	0/0:6:6:214:0:0:0,-1.80618,-10
+1	94699	.	G	A	22.3	.	AB=0.24;ABP=17.6895;AC=3;AF=0.0882353;AN=34;AO=9;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:45:45:1655:0:0:0,-10,-10	0/1:6:4:144:2:72:-6.20991,0,-10	0/0:11:11:414:0:0:0,-3.31133,-10
+1	94725	.	C	T	51.0	.	AB=1;ABP=13.8677;AC=3;AF=0.107143;AN=28;AO=9;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:42:42:1539:0:0:0,-10,-10	0/0:3:3:114:0:0:0,-0.90309,-10	0/0:13:12:474:1:9:0,-1.89945,-10
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+1	94991	.	G	A	683.9	.	AB=0.351351;ABP=17.2129;AC=2;AF=0.111111;AN=18;AO=26;CIGAR=1X;TYPE=snp;mapq=40.1429;coverage=7;xdp2=3,4	GT:DP:RO:QR:AO:QA:GL	0/1:74:48:1608:26:918:-10,0,-10	.:.:.:.:.:.:.	0/0:26:26:868:0:0:0,-7.82678,-10
+1	95006	.	A	T	1209.5	.	AB=0.274611;ABP=88.1703;AC=16;AF=0.470588;AN=34;AO=71;CIGAR=1X;TYPE=snp;mapq=39;coverage=2;xdp2=1,1	GT:DP:RO:QR:AO:QA:GL	0/0:86:83:2850:3:106:0,-10,-10	0/1:4:0:0:4:152:-10,-1.20412,0	0/1:33:29:1025:4:128:-6.51795,0,-10
+1	95011	.	T	G	674.6	.	AB=0.47619;ABP=3.94093;AC=12;AF=0.352941;AN=34;AO=111;CIGAR=1X1M;TYPE=snp;mapq=21.6667;coverage=3;xdp2=2,1	GT:DP:RO:QR:AO:QA:GL	0/0:84:79:2791:3:19:0,-10,-10	0/1:10:3:49:6:64:-4.76644,0,-3.48501	0/0:34:29:1054:3:26:0,-3.75548,-10
+1	95054	.	G	A	201.1	.	AB=0.25;ABP=24.725;AC=1;AF=0.0294118;AN=34;AO=10;CIGAR=1X;TYPE=snp;mapq=28.6667;coverage=3;xdp2=1,2	GT:DP:RO:QR:AO:QA:GL	0/0:85:85:2938:0:0:0,-10,-10	0/0:16:16:558:0:0:0,-4.81648,-10	0/0:49:49:1618:0:0:0,-10,-10
+1	95611	.	G	A	36.8	.	AB=0.235294;ABP=13.3567;AC=1;AF=0.0294118;AN=34;AO=4;CIGAR=1X;TYPE=snp;mapq=20;coverage=3;xdp2=3,0	GT:DP:RO:QR:AO:QA:GL	0/0:17:17:620:0:0:0,-5.11751,-10	0/0:2:2:70:0:0:0,-0.60206,-6.65	0/0:7:7:252:0:0:0,-2.10721,-10
+1	96594	.	C	T	953.0	.	AB=0.355556;ABP=19.3205;AC=2;AF=0.111111;AN=18;AO=32;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:90:58:2040:32:1200:-10,0,-10	.:.:.:.:.:.:.	0/0:18:18:623:0:0:0,-5.41854,-10
+1	97164	.	A	G	353.7	.	AB=0;ABP=0;AC=12;AF=1;AN=12;AO=12;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:3:0:0:3:102:-9.52,-0.90309,0	.:.:.:.:.:.:.	1/1:1:0:0:1:35:-3.5,-0.30103,0
+1	97587	.	G	C	303.7	.	AB=0.285714;ABP=19.7617;AC=1;AF=0.05;AN=20;AO=12;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:42:30:1120:12:451:-10,0,-10	0/0:1:1:40:0:0:0,-0.30103,-4	0/0:21:21:796:0:0:0,-6.32163,-10
+1	97661	.	T	C	33.4	.	AB=0.3;ABP=6.48466;AC=1;AF=0.0333333;AN=30;AO=5;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:19:18:629:1:41:0,-0.340816,-10	0/0:2:2:74:0:0:0,-0.60206,-7.03	0/0:8:8:292:0:0:0,-2.40824,-10
+1	97937	.	T	A	12.3	.	AB=0.428571;ABP=3.32051;AC=2;AF=0.0588235;AN=34;AO=5;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:26:26:899:0:0:0,-7.82678,-10	0/0:3:3:113:0:0:0,-0.90309,-10	0/0:7:7:248:0:0:0,-2.10721,-10
+1	97953	.	A	G	1000.6	.	AB=0.401709;ABP=12.8283;AC=13;AF=0.382353;AN=34;AO=48;CIGAR=1X;TYPE=snp;mapq=20.5;coverage=2;xdp2=2,0	GT:DP:RO:QR:AO:QA:GL	0/0:32:32:1102:0:0:0,-9.63296,-10	0/1:6:4:155:2:77:-6.68491,0,-10	0/0:10:10:355:0:0:0,-3.0103,-10
+1	98683	.	G	A	610.5	.	AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp;AC_AFR=0;AC_AMR=0;AC_EAS=0	GT:DP:RO:QR:AO:QA:GL	0/0:73:71:2641:2:78:0,-10,-10	0/0:1:0:0:1:34:-3.4,-0.30103,0	0/1:33:29:1059:4:139:-7.53545,0,-10
+1	98688	.	G	<DEL>	610.5	.	CIEND=-4,2;SVLEN=10;AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:73:71:2641:2:78:0,-10,-10	0/0:1:0:0:1:34:-3.4,-0.30103,0	0/1:33:29:1059:4:139:-7.53545,0,-10
+2	98688	.	G	<DEL>	610.5	.	CIEND=-4,2;SVLEN=10;AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:73:71:2641:2:78:0,-10,-10	0/0:1:0:0:1:34:-3.4,-0.30103,0	0/1:33:29:1059:4:139:-7.53545,0,-10
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfanno.xml	Thu Jan 21 10:33:49 2021 +0000
@@ -0,0 +1,266 @@
+<?xml version="1.0"?>
+<tool id="vcfanno" name="vcfanno" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>VCF annotation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="xrefs"/>
+
+    <expand macro="requirements"/>
+
+    <expand macro="version_command"/>
+
+    <!--
+    In future versions - figure out how to safely add in lua support without posing security risk
+    (Should be doable but requires writing some lua unfortunately to make custom sandboxes)
+     -->
+    <command detect_errors="exit_code"><![CDATA[
+    ln -s '$config_toml' config.toml &&
+    ln -s '$input_vcf' input.vcf &&
+
+    #for $i, $annotation in enumerate($annotations):
+        #set $ext = str($annotation.type.type_select)
+        ln -s '$annotation.type.annotation' 'input_${i}.${ext}' &&
+        ### These sets of conversions etc shouldn't be necessary but the vcfanno in Galaxy looks for an index file regardless of compression for some reason and if not present fails.
+        #if $ext == 'vcf' or $ext == 'bed':
+            bgzip 'input_${i}.${ext}' &&
+            #set $ext = $ext + ".gz"
+        #end if
+        #if '.gz' in $ext[-3:]:
+            tabix -p vcf 'input_${i}.${ext}' &&
+        #elif $ext == 'bam':
+            ln -s '${annotation.type.annotation.metadata.bam_index}' input_${i}.bam.bai &&
+        #end if
+    #end for
+    vcfanno -p \${GALAXY_SLOTS:-4}
+#if $ends:
+    '$ends'
+#end if
+#if $permissive_overlap:
+    '$permissive_overlap'
+#end if
+    config.toml
+    input.vcf
+    >
+    '$out_vcf'
+    ]]></command>
+    <configfiles>
+        <configfile name="config_toml">#
+#for $i, $annotation in enumerate($annotations):
+    #set $ext = $annotation.type.type_select
+    #if $ext == 'vcf' or $ext == 'bed':
+        #set $ext = $ext + ".gz"
+    #end if
+    #if $ext == 'vcf.gz' or $ext == 'bam':
+        #set $annotation_names = list()
+        #set $annotation_fields = list()
+        #set $annotation_ops = list()
+        #for $field in $annotation.type.fields:
+            #silent $annotation_names.append('"%s"' %(str($field.name)))
+            #silent $annotation_fields.append('"%s"' %(str($field.field)))
+            #silent $annotation_ops.append('"%s"' %(str($field.op)))
+        #end for
+        #set $names = "names= [%s]" % (", ".join($annotation_names))
+        #set $fields = "fields= [%s]" % (", ".join($annotation_fields))
+        #set $ops = "ops= [%s]" % (", ".join($annotation_ops))
+    #elif $ext == 'bed.gz':
+        #set $annotation_names = list()
+        #set $annotation_columns = list()
+        #set $annotation_ops = list()
+        #for $field in $annotation.type.fields:
+            #silent $annotation_names.append('"%s"' %(str($field.name)))
+            #silent $annotation_columns.append( str($field.columns))
+            #silent $annotation_ops.append('"%s"' %(str($field.op)))
+        #end for
+        #set $names = "names= [%s]" % (", ".join($annotation_names))
+        #set $fields = "columns= [%s]" % (", ".join($annotation_columns))
+        #set $ops = "ops= [%s]" % (", ".join($annotation_ops))
+    #end if
+[[annotation]]
+file="input_${i}.${ext}"
+${names}
+${fields}
+${ops}
+
+#end for
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="input_vcf" type="data" format="vcf,vcf_bgzip" label="VCF to be annotated"/>
+        <param argument="-ends" type="boolean" checked="false" truevalue="-ends" falsevalue="" label="annotate the start and end as well as the interval itself?"/>
+        <param argument="-permissive-overlap" type="boolean" checked="false" truevalue="-permissive-overlap" falsevalue="" label="annotate with an overlapping variant even it doesn't share the same ref and alt alleles." help="Default is to require exact match between variants."/>
+        <repeat name="annotations" title="Input annotations" min="1">
+            <conditional name="type">
+                <param name="type_select" type="select">
+                    <option value="vcf" selected="true">VCF</option>
+                    <option value="vcf.gz">VCF.bgzip</option>
+                    <option value="bed">BED</option>
+                    <option value="bam">BAM</option>
+                </param>
+                <when value="vcf">
+                    <param name="annotation" type="data" format="vcf" label="Annotation file"/>
+                    <repeat name="fields" title="Fields" min="1">
+                        <param name="name" type="text"/>
+                        <param name="field" type="text" help="ID and FILTER are special fields that pull the ID and FILTER columns from the VCF"/>
+                        <param name="op" type="select" label="Op" help="In most cases, we will have a single annotation entry for each entry (variant) in the query VCF, in which case the self op is the best choice. However, it is possible that there will be multiple annotations from a single annotation file--in this case, the op determines how the many values are reduced. In nearly all cases, if you are annotating with a VCF, use self">
+                            <expand macro="ops"/>
+                        </param>
+                    </repeat>
+                </when>
+                <when value="vcf.gz">
+                    <param name="annotation" type="data" format="vcf_bgzip" label="Annotation file"/>
+                    <repeat name="fields" title="Fields" min="1">
+                        <param name="name" type="text"/>
+                        <param name="field" type="text" help="ID and FILTER are special fields that pull the ID and FILTER columns from the VCF"/>
+                        <param name="op" type="select" label="Op" help="In most cases, we will have a single annotation entry for each entry (variant) in the query VCF, in which case the self op is the best choice. However, it is possible that there will be multiple annotations from a single annotation file--in this case, the op determines how the many values are reduced. In nearly all cases, if you are annotating with a VCF, use self">
+                            <expand macro="ops"/>
+                        </param>
+                    </repeat>
+                </when>
+                <when value="bed">
+                    <param name="annotation" type="data" format="bed" label="Annotation file"/>
+                    <repeat name="fields" title="Fields" min="1">
+                        <param name="name" type="text"/>
+                        <param name="columns" type="text" help="(1-based) column number from which to pull the value for the op"/>
+                        <param name="op" type="select" label="Op">
+                            <expand macro="ops"/>
+                        </param>
+                    </repeat>
+                </when>
+                <when value="bam">
+                    <param name="annotation" type="data" format="bam" label="Annotation file"/>
+                    <repeat name="fields" title="Fields" min="1">
+                        <param name="name" type="text"/>
+                        <param name="field" type="select" help="Field in the BAM to pull value from">
+                            <option value="depth">Depth (count)</option>
+                            <option value="coverage">Coverage</option>
+                            <option value="mapq">mapq (mapping quality)</option>
+                            <option value="seq">seq</option>
+                            <option value="DP2">DP2</option>
+                        </param>
+                        <param name="op" type="select" label="Op" help="Op to perform on the field. Note: DP2 field always will result in DP2 op">
+                            <expand macro="ops"/>
+                        </param>
+                    </repeat>
+                </when>
+            </conditional>
+        </repeat>
+        <!-- <repeat name="postannotations" title="Input postannotations">
+        </repeat> -->
+        <!-- Until we figure out lua sanitization there's really no point to adding this either-->
+    </inputs>
+    <outputs>
+        <!-- standard -->
+        <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="1">
+            <param name="input_vcf" value="query.vcf.gz" ftype="vcf_bgzip"/>
+            <repeat name="annotations">
+                <conditional name="type">
+                    <param name="type_select" value="vcf.gz" />
+                    <param name="annotation" value="exac.vcf.gz" ftype="vcf_bgzip"/>
+                    <repeat name="fields">
+                        <param name="name" value="AC_AFR" />
+                        <param name="field" value="AC_AFR" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="AC_AMR" />
+                        <param name="field" value="AC_AMR" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="AC_EAS" />
+                        <param name="field" value="AC_EAS" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="ID" />
+                        <param name="field" value="ID" />
+                        <param name="op" value="first" />
+                    </repeat>
+                </conditional>
+            </repeat>
+            <repeat name="annotations">
+                <conditional name="type">
+                    <param name="type_select" value="bam" />
+                    <param name="annotation" value="ex.bam" />
+                    <repeat name="fields">
+                        <param name="name" value="mapq" />
+                        <param name="field" value="mapq" />
+                        <param name="op" value="mean" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="coverage" />
+                        <param name="field" value="coverage" />
+                        <param name="op" value="sum" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="xdp2" />
+                        <param name="field" value="DP2" />
+                        <param name="op" value="self" />
+                    </repeat>
+                </conditional>
+            </repeat>
+            <repeat name="annotations">
+                <conditional name="type">
+                    <param name="type_select" value="bed" />
+                    <param name="annotation" value="fitcons.bed" />
+                    <repeat name="fields">
+                        <param name="name" value="lua_start" />
+                        <param name="columns" value="4" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="lua_end" />
+                        <param name="columns" value="4" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="lua_len" />
+                        <param name="columns" value="4" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="lua_mean" />
+                        <param name="columns" value="4" />
+                        <param name="op" value="first" />
+                    </repeat>
+                    <repeat name="fields">
+                        <param name="name" value="lua_loc" />
+                        <param name="columns" value="4" />
+                        <param name="op" value="first" />
+                    </repeat>
+                </conditional>
+            </repeat>
+            <output name="out_vcf" file="vcfanno_result.vcf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+Note this version of vcfanno does not support lua code functionality
+
+**Input**
+
+- VCF file to be annotated
+
+- BAM / BED / VCF files to annotate with
+
+**Output**
+
+- Annotated VCF
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>