Mercurial > repos > bgruening > nanopolish_variants

comparison test-data/t2-variants.vcf @ 5:63af3144371a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
author bgruening
date Fri, 29 May 2020 13:29:14 -0400
parents bc79b5b0fe04
children
comparison
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4:de5b3d8f5b90 5:63af3144371a
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##nanopolish_window=tig00000001:198000-202000 2 ##nanopolish_window=tig00000001:198000-202000
3 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> 3 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
4 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> 4 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
5 ##INFO=<ID=SupportFractionByStrand,Number=2,Type=Float,Description="Fraction of event-space reads that support the variant for each strand">
5 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> 6 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
6 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> 7 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
7 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> 8 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
8 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position"> 9 ##INFO=<ID=StrandSupport,Number=4,Type=Integer,Description="Number of reads supporting the REF and ALT allele, by strand">
10 ##INFO=<ID=StrandFisherTest,Number=1,Type=Integer,Description="Strand bias fisher test">
11 ##INFO=<ID=SOR,Number=1,Type=Float,Description="StrandOddsRatio test from GATK">
12 ##INFO=<ID=RefContext,Number=1,Type=String,Description="The reference sequence context surrounding the variant call">
13 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Float,Description="The fraction of reads supporting A,C,G,T at this position">
9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 14 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
10 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 15 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
11 tig00000001 198435 . G A 22.3 PASS BaseCalledReadsWithVariant=10;BaseCalledFraction=0.238095;TotalReads=42;AlleleCount=1;SupportFraction=0.388965;SupportFractionByBase=0.210,0.030,0.718,0.041 GT 0/1