Mercurial > repos > iuc > deepvariant

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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:
rev   line source
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.2
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
14 ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
15 ##DeepVariant_version=1.5.0
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
16 ##contig=<ID=K03455,length=9719>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
17 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
18 K03455 2652 . G A 27.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:201:0,200:0.995025:27,33,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
19 K03455 2660 . T C 30.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:213:0,213:1:30,34,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
20 K03455 2664 . A G 24.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:238:0,238:1:24,32,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
21 K03455 2669 . G A 29.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:258:0,250:0.968992:29,36,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
22 K03455 2720 . T C 42.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:37:384:0,380:0.989583:42,38,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
23 K03455 2797 . G A 44.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:669:0,666:0.995516:44,46,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
24 K03455 2848 . T TA 46.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:38:820:85,704:0.858537:46,38,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
25 K03455 2874 . C T 36.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:777:1,756:0.972973:36,34,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
26 K03455 2882 . G T 37.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:33:737:9,721:0.97829:37,34,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
27 K03455 2894 . T C 32.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:30:728:1,717:0.98489:32,34,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
28 K03455 2906 . C T 32.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:653:2,650:0.995406:32,31,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
29 K03455 2913 . G A 41.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:639:1,638:0.998435:41,42,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
30 K03455 2987 . C T 11.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:11:235:0,234:0.995745:11,23,0
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
31 K03455 3020 . A G 0.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:8:100:0,100:1:0,26,7
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
32 K03455 3042 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:37:12:9,3:0.25:0,41,39