Mercurial > repos > iuc > deepvariant

annotate test-data/output.vcf @ 0:7608209110d3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
author iuc
date Mon, 06 Sep 2021 17:34:08 +0000
parents
children 98fe794d2ec0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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1 ##fileformat=VCFv4.2
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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2 ##FILTER=<ID=PASS,Description="All filters passed">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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3 ##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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4 ##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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5 ##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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6 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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8 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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9 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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10 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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11 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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12 ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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13 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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14 ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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15 ##DeepVariant_version=1.2.0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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16 ##contig=<ID=K03455,length=9719>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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17 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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18 K03455 2652 . G A 23.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:201:0,200:0.995025:23,45,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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19 K03455 2660 . T C 25.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:25:213:0,213:1:25,45,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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20 K03455 2664 . A G 21.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:238:0,238:1:21,45,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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21 K03455 2669 . G A 20.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:20:258:0,250:0.968992:20,43,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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22 K03455 2720 . T C 31.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:384:0,380:0.989583:31,47,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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23 K03455 2797 . G A 39.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:669:0,666:0.995516:39,54,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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24 K03455 2848 . T TA 41.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:820:85,704:0.858537:41,43,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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25 K03455 2874 . C T 32 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:777:1,756:0.972973:32,45,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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26 K03455 2882 . G T 33.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:33:737:9,721:0.97829:33,49,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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27 K03455 2894 . T C 28.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:28:728:1,717:0.98489:28,51,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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28 K03455 2906 . C T 23.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:653:2,650:0.995406:23,53,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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29 K03455 2913 . G A 27.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:639:1,638:0.998435:27,53,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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30 K03455 2987 . C T 16.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:16:235:0,234:0.995745:16,38,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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31 K03455 3020 . A G 3.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:100:0,100:1:0,24,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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32 K03455 3042 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:37:12:9,3:0.25:0,40,39