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annotate test-data/passed.somatic.snvs.vcf @ 13:bce06de6cea2

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modified help section
author mini
date Wed, 01 Oct 2014 10:40:22 +0200
parents 87568e5a7d4f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 ##fileformat=VCFv4.1
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2 ##fileDate=20130116
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3 ##source=strelka
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4 ##source_version=2.0.2-29-ged3977a
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5 ##startTime=Wed Jan 16 19:42:09 2013
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6 ##reference=file:///home/csaunders/devel/strelka_workflow/scratch/strelka_workflow-1.0.0-10-g37f7f70/install/bin/demo/data/chr20_860k_only.fa
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7 ##contig=<ID=chr20,length=63025520>
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8 ##content=strelka somatic snv calls
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9 ##germlineSnvTheta=0.001
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10 ##priorSomaticSnvRate=1e-06
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11 ##INFO=<ID=QSS,Number=1,Type=Integer,Description="Quality score for any somatic snv, ie. for the ALT allele to be present at a significantly different frequency in the tumor and normal">
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12 ##INFO=<ID=TQSS,Number=1,Type=Integer,Description="Data tier used to compute QSS">
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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}.">
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14 ##INFO=<ID=QSS_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
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15 ##INFO=<ID=TQSS_NT,Number=1,Type=Integer,Description="Data tier used to compute QSS_NT">
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16 ##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states">
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17 ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1 (used+filtered)">
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19 ##FORMAT=<ID=FDP,Number=1,Type=Integer,Description="Number of basecalls filtered from original read depth for tier1">
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20 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Number of reads with deletions spanning this site at tier1">
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21 ##FORMAT=<ID=SUBDP,Number=1,Type=Integer,Description="Number of reads below tier1 mapping quality threshold aligned across this site">
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22 ##FORMAT=<ID=AU,Number=2,Type=Integer,Description="Number of 'A' alleles used in tiers 1,2">
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23 ##FORMAT=<ID=CU,Number=2,Type=Integer,Description="Number of 'C' alleles used in tiers 1,2">
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24 ##FORMAT=<ID=GU,Number=2,Type=Integer,Description="Number of 'G' alleles used in tiers 1,2">
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25 ##FORMAT=<ID=TU,Number=2,Type=Integer,Description="Number of 'T' alleles used in tiers 1,2">
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26 ##FILTER=<ID=BCNoise,Description="Fraction of basecalls filtered at this site in either sample is at or above 0.4">
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27 ##FILTER=<ID=SpanDel,Description="Fraction of reads crossing site with spanning deletions in either sample exceeeds 0.75">
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28 ##FILTER=<ID=QSS_ref,Description="Normal sample is not homozygous ref or ssnv Q-score < 15, ie calls with NT!=ref or QSS_NT < 15">
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29 ##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
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30 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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31 chr20 863271 . A G . PASS NT=ref;QSS=40;QSS_NT=40;SGT=AA->AG;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 26:0:0:0:26,26:0,0:0,0:0,0 18:0:0:0:8,8:0,0:10,10:0,0
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32 chr20 863508 . A G . PASS NT=ref;QSS=68;QSS_NT=68;SGT=AA->AG;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 39:0:0:0:39,39:0,0:0,0:0,0 23:0:0:0:11,11:0,0:12,12:0,0
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33 chr20 863706 . C T . PASS NT=ref;QSS=109;QSS_NT=83;SGT=CC->TT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 33:2:0:0:0,0:31,33:0,0:0,0 19:0:0:0:0,0:0,0:0,0:19,19
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34 chr20 863744 . C T . PASS NT=ref;QSS=43;QSS_NT=43;SGT=CC->CT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 27:0:0:0:0,0:27,27:0,0:0,0 21:0:0:0:0,0:9,9:0,0:12,12
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35 chr20 863846 . C T . PASS NT=ref;QSS=27;QSS_NT=27;SGT=CC->CT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 21:0:0:0:0,0:21,21:0,0:0,0 25:0:0:0:0,0:16,16:0,0:9,9
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36 chr20 864074 . T C . PASS NT=ref;QSS=39;QSS_NT=39;SGT=TT->CT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 26:0:0:0:0,0:0,0:0,0:26,26 25:0:0:0:0,0:11,11:0,0:14,14
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37 chr20 864199 . G A . PASS NT=ref;QSS=58;QSS_NT=58;SGT=GG->AG;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 33:0:0:0:0,0:0,0:33,33:0,0 29:0:0:0:14,14:0,0:15,15:0,0
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38 chr20 864301 . G T . PASS NT=ref;QSS=41;QSS_NT=41;SGT=GG->GT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 27:1:0:0:0,0:0,0:26,27:0,0 30:0:0:0:0,0:0,0:12,12:18,18
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39 chr20 864455 . T C . PASS NT=ref;QSS=138;QSS_NT=79;SGT=TT->CC;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 28:0:0:0:0,0:0,0:0,0:28,28 33:1:0:0:0,0:32,33:0,0:0,0
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40 chr20 864512 . A G . PASS NT=ref;QSS=43;QSS_NT=43;SGT=AA->AG;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 26:1:0:0:25,26:0,0:0,0:0,0 40:0:0:0:14,14:0,0:26,27:0,0
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41 chr20 864640 . C T . PASS NT=ref;QSS=147;QSS_NT=86;SGT=CC->TT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 35:0:0:0:0,0:35,35:0,0:0,0 28:0:0:0:0,0:0,0:0,0:28,28
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42 chr20 864660 . G T . PASS NT=ref;QSS=115;QSS_NT=82;SGT=GG->TT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 30:0:0:0:0,0:0,0:30,30:0,0 22:0:0:0:0,0:0,0:0,0:22,22
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43 chr20 865366 . G T . PASS NT=ref;QSS=114;QSS_NT=74;SGT=GG->TT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 26:0:0:0:0,0:0,0:26,26:0,0 26:0:0:0:0,0:0,0:0,0:26,26
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44 chr20 865537 . C T . PASS NT=ref;QSS=40;QSS_NT=40;SGT=CC->CT;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 30:0:0:0:0,0:30,30:0,0:0,0 32:0:0:0:0,0:21,21:0,0:11,11