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annotate test-data/output.g.vcf @ 4:63b68fe4af85 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit d936ef547007b54a536787384cae90e98af2aede
author iuc
date Tue, 05 Mar 2024 08:10:46 +0000
parents 918c8b94c8d8
children
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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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.">
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918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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15 ##DeepVariant_version=1.5.0
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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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"
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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"
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18 K03455 1 . T <*> 0 . END=1000 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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19 K03455 1001 . G <*> 0 . END=2000 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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20 K03455 2001 . T <*> 0 . END=2597 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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21 K03455 2598 . G <*> 0 . END=2598 GT:GQ:MIN_DP:PL ./.:0:2:59,6,0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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22 K03455 2599 . A <*> 0 . END=2603 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59
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918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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23 K03455 2604 . CCA C,<*> 3.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:2:0,2,0:1,0:0,9,0,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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24 K03455 2607 . A <*> 0 . END=2607 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59
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918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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25 K03455 2608 . A T,<*> 6.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:2:0,2,0:1,0:4,9,0,990,990,990
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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26 K03455 2609 . A T,<*> 5.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:4:2:0,2,0:1,0:3,9,0,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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27 K03455 2610 . G <*> 0 . END=2612 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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28 K03455 2613 . A T,<*> 0.9 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:2:0,2,0:1,0:0,10,8,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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29 K03455 2614 . A <*> 0 . END=2614 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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30 K03455 2615 . A <*> 0 . END=2615 GT:GQ:MIN_DP:PL 0/0:15:5:0,15,149
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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31 K03455 2616 . C <*> 0 . END=2616 GT:GQ:MIN_DP:PL ./.:0:7:8,0,158
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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32 K03455 2617 . A <*> 0 . END=2617 GT:GQ:MIN_DP:PL ./.:0:6:11,0,131
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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33 K03455 2618 . A <*> 0 . END=2618 GT:GQ:MIN_DP:PL 0/0:18:6:0,18,179
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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34 K03455 2619 . T <*> 0 . END=2619 GT:GQ:MIN_DP:PL 0/0:21:7:0,21,209
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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35 K03455 2620 . G <*> 0 . END=2620 GT:GQ:MIN_DP:PL 0/0:39:13:0,39,389
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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36 K03455 2621 . G <*> 0 . END=2651 GT:GQ:MIN_DP:PL 0/0:50:49:0,147,1469
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918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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37 K03455 2652 . G A,<*> 27.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:201:0,201,0:1,0:27,34,0,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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38 K03455 2653 . T <*> 0 . END=2659 GT:GQ:MIN_DP:PL 0/0:50:201:0,300,2999
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918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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39 K03455 2660 . T C,<*> 30.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:213:0,213,0:1,0:30,35,0,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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40 K03455 2661 . T <*> 0 . END=2663 GT:GQ:MIN_DP:PL 0/0:50:213:0,300,2999
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
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41 K03455 2664 . A G,<*> 24.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:238:0,238,0:1,0:24,32,0,990,990,990
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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42 K03455 2665 . C <*> 0 . END=2668 GT:GQ:MIN_DP:PL 0/0:50:240:0,300,2999
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
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43 K03455 2669 . G A,<*> 30.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:250:0,250,0:1,0:30,35,0,990,990,990