view test-data/passed.somatic.indels.vcf @ 9:0e8e6011082b

Strelka Workflow 0.0.2

##fileformat=VCFv4.1
##fileDate=20130116
##source=strelka
##source_version=2.0.2-29-ged3977a
##startTime=Wed Jan 16 19:42:09 2013
##reference=file:///home/csaunders/devel/strelka_workflow/scratch/strelka_workflow-1.0.0-10-g37f7f70/install/bin/demo/data/chr20_860k_only.fa
##contig=<ID=chr20,length=63025520>
##content=strelka somatic indel calls
##germlineIndelTheta=0.0001
##priorSomaticIndelRate=1e-06
##INFO=<ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal">
##INFO=<ID=TQSI,Number=1,Type=Integer,Description="Data tier used to compute QSI">
##INFO=<ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
##INFO=<ID=QSI_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
##INFO=<ID=TQSI_NT,Number=1,Type=Integer,Description="Data tier used to compute QSI_NT">
##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states">
##INFO=<ID=RU,Number=1,Type=String,Description="Smallest repeating sequence unit in inserted or deleted sequence">
##INFO=<ID=RC,Number=1,Type=Integer,Description="Number of times RU repeats in the reference allele">
##INFO=<ID=IC,Number=1,Type=Integer,Description="Number of times RU repeats in the indel allele">
##INFO=<ID=IHP,Number=1,Type=Integer,Description="Largest reference interupted homopolymer length intersecting with the indel">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
##INFO=<ID=OVERLAP,Number=0,Type=Flag,Description="Somatic indel possibly overlaps a second indel.">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1">
##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
##FILTER=<ID=Repeat,Description="Sequence repeat of more than 8x in the reference sequence">
##FILTER=<ID=iHpol,Description="Indel overlaps an interupted homopolymer longer than 14x in the reference sequence">
##FILTER=<ID=BCNoise,Description="Average fraction of filtered basecalls within 50 bases of the indel exceeds 0.3">
##FILTER=<ID=QSI_ref,Description="Normal sample is not homozygous ref or sindel Q-score < 30, ie calls with NT!=ref or QSI_NT < 30">
##cmdline=/home/csaunders/devel/strelka_workflow/scratch/strelka_workflow-1.0.0-10-g37f7f70/install/libexec/consolidateResults.pl --config=/home/csaunders/devel/strelka_workflow/scratch/strelka_workflow-1.0.0-10-g37f7f70/install/bin/demo/strelkaDemoAnalysis/config/run.config.ini
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
chr20	863148	.	C	CTAT	.	PASS	IC=2;IHP=3;NT=ref;QSI=35;QSI_NT=35;RC=1;RU=TAT;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	28:28:26,26:0,0:2,2:26.34:0.00:0.00	20:20:10,10:7,7:3,3:20.83:0.00:0.00
chr20	865664	.	TC	T	.	PASS	IC=3;IHP=8;NT=ref;QSI=39;QSI_NT=39;RC=4;RU=C;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	22:22:22,22:0,0:0,0:24.92:0.00:0.00	41:41:18,18:20,20:2,2:36.47:0.05:0.00