Mercurial > repos > mini > strelka
comparison test-data/all.somatic.indels.vcf @ 6:87568e5a7d4f
Testing strelka version 0.0.1
| author | mini |
|---|---|
| date | Fri, 26 Sep 2014 13:24:13 +0200 |
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| 5:07cbbd662111 | 6:87568e5a7d4f |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##fileDate=20130116 | |
| 3 ##source=strelka | |
| 4 ##source_version=2.0.2-29-ged3977a | |
| 5 ##startTime=Wed Jan 16 19:42:09 2013 | |
| 6 ##reference=file:///home/csaunders/devel/strelka_workflow/scratch/strelka_workflow-1.0.0-10-g37f7f70/install/bin/demo/data/chr20_860k_only.fa | |
| 7 ##contig=<ID=chr20,length=63025520> | |
| 8 ##content=strelka somatic indel calls | |
| 9 ##germlineIndelTheta=0.0001 | |
| 10 ##priorSomaticIndelRate=1e-06 | |
| 11 ##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"> | |
| 12 ##INFO=<ID=TQSI,Number=1,Type=Integer,Description="Data tier used to compute QSI"> | |
| 13 ##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}."> | |
| 14 ##INFO=<ID=QSI_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT"> | |
| 15 ##INFO=<ID=TQSI_NT,Number=1,Type=Integer,Description="Data tier used to compute QSI_NT"> | |
| 16 ##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states"> | |
| 17 ##INFO=<ID=RU,Number=1,Type=String,Description="Smallest repeating sequence unit in inserted or deleted sequence"> | |
| 18 ##INFO=<ID=RC,Number=1,Type=Integer,Description="Number of times RU repeats in the reference allele"> | |
| 19 ##INFO=<ID=IC,Number=1,Type=Integer,Description="Number of times RU repeats in the indel allele"> | |
| 20 ##INFO=<ID=IHP,Number=1,Type=Integer,Description="Largest reference interupted homopolymer length intersecting with the indel"> | |
| 21 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 22 ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation"> | |
| 23 ##INFO=<ID=OVERLAP,Number=0,Type=Flag,Description="Somatic indel possibly overlaps a second indel."> | |
| 24 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1"> | |
| 25 ##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2"> | |
| 26 ##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2"> | |
| 27 ##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2"> | |
| 28 ##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2"> | |
| 29 ##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases"> | |
| 30 ##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases"> | |
| 31 ##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases"> | |
| 32 ##FILTER=<ID=Repeat,Description="Sequence repeat of more than 8x in the reference sequence"> | |
| 33 ##FILTER=<ID=iHpol,Description="Indel overlaps an interupted homopolymer longer than 14x in the reference sequence"> | |
| 34 ##FILTER=<ID=BCNoise,Description="Average fraction of filtered basecalls within 50 bases of the indel exceeds 0.3"> | |
| 35 ##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"> | |
| 36 ##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 | |
| 37 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR | |
| 38 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 | |
| 39 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 |