Mercurial > repos > bgruening > nanopolish_methylation
diff test-data/t3_variants.vcf @ 5:12efe2f03697 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
| author | bgruening |
|---|---|
| date | Fri, 29 May 2020 13:30:11 -0400 |
| parents | 02e3c674d917 |
| children |
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--- a/test-data/t3_variants.vcf Sun Jun 23 05:54:36 2019 -0400 +++ b/test-data/t3_variants.vcf Fri May 29 13:30:11 2020 -0400 @@ -2,20 +2,26 @@ ##nanopolish_window=tig00000001:200000-202000 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=SupportFractionByStrand,Number=2,Type=Float,Description="Fraction of event-space reads that support the variant for each strand"> ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##INFO=<ID=StrandSupport,Number=4,Type=Integer,Description="Number of reads supporting the REF and ALT allele, by strand"> +##INFO=<ID=StrandFisherTest,Number=1,Type=Integer,Description="Strand bias fisher test"> +##INFO=<ID=SOR,Number=1,Type=Float,Description="StrandOddsRatio test from GATK"> +##INFO=<ID=RefContext,Number=1,Type=String,Description="The reference sequence context surrounding the variant call"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 -tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 -tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 -tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 -tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 -tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1 -tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 -tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 -tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 -tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 -tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 -tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 +tig00000001 200061 . T TA 36.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.334093;SupportFractionByStrand=0.354592,0.312974;StrandSupport=22,23,12,10;StrandFisherTest=1;SOR=0.818803;RefContext=TTGAATAAAAA GT 1 +tig00000001 200180 . C CA 45.3 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.637264;SupportFractionByStrand=0.75298,0.521547;StrandSupport=8,16,25,17;StrandFisherTest=9;SOR=0.838011;RefContext=GAGGGCAAAAT GT 1 +tig00000001 200389 . T TA 33.2 PASS TotalReads=64;AlleleCount=1;SupportFraction=0.618644;SupportFractionByStrand=0.625518,0.611327;StrandSupport=12,12,21,19;StrandFisherTest=0;SOR=0.75277;RefContext=CAACATAAAAA GT 1 +tig00000001 200484 . G GA 36.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.600783;SupportFractionByStrand=0.593951,0.607834;StrandSupport=13,12,19,19;StrandFisherTest=0;SOR=0.641151;RefContext=TGCGCGAAAAG GT 1 +tig00000001 200672 . T TA 106.6 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.41069;SupportFractionByStrand=0.507758,0.304229;StrandSupport=17,22,17,9;StrandFisherTest=9;SOR=1.30379;RefContext=AGTAATAAAAC GT 1 +tig00000001 200776 . C CA 96.0 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.343276;SupportFractionByStrand=0.355235,0.330195;StrandSupport=23,21,12,11;StrandFisherTest=0;SOR=0.798543;RefContext=TTTCGCAAAAT GT 1 +tig00000001 200796 . T TAAA 163.5 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.273151;SupportFractionByStrand=0.306456,0.237765;StrandSupport=24,24,10,8;StrandFisherTest=2;SOR=0.992084;RefContext=GGGTGTAAAAG GT 1 +tig00000001 201007 . A AG 45.9 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.343541;SupportFractionByStrand=0.341375,0.345774;StrandSupport=22,21,11,11;StrandFisherTest=0;SOR=0.674028;RefContext=ACAAAAGGGGA GT 1 +tig00000001 201216 . A AT 101.1 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.443739;SupportFractionByStrand=0.364917,0.520243;StrandSupport=21,16,12,18;StrandFisherTest=5;SOR=0.983873;RefContext=TGGTGATTTTA GT 1 +tig00000001 201273 . G GT 39.5 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.343151;SupportFractionByStrand=0.346289,0.340197;StrandSupport=21,22,11,12;StrandFisherTest=0;SOR=0.666106;RefContext=TGGCGGTTTTT GT 1 +tig00000001 201554 . G GC 64.8 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.386911;SupportFractionByStrand=0.359184,0.414639;StrandSupport=24,22,14,16;StrandFisherTest=1;SOR=0.76503;RefContext=TCGGTGCCCCA GT 1 +tig00000001 201588 . C CG 135.2 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.375988;SupportFractionByStrand=0.37007,0.382065;StrandSupport=24,23,14,14;StrandFisherTest=0;SOR=0.655214;RefContext=CCCGGCGGGTG GT 1 +tig00000001 201712 . C CA 34.7 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.608624;SupportFractionByStrand=0.68759,0.529659;StrandSupport=12,17,25,20;StrandFisherTest=6;SOR=0.748413;RefContext=CCGGACAAAAC GT 1