Mercurial > repos > iuc > deepvariant
view test-data/output.g.vcf @ 4:63b68fe4af85 draft default tip
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 |
line wrap: on
line source
##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference."> ##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold."> ##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call."> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block."> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions."> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer"> ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer."> ##DeepVariant_version=1.5.0 ##contig=<ID=K03455,length=9719> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 K03455 1 . T <*> 0 . END=1000 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0 K03455 1001 . G <*> 0 . END=2000 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0 K03455 2001 . T <*> 0 . END=2597 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0 K03455 2598 . G <*> 0 . END=2598 GT:GQ:MIN_DP:PL ./.:0:2:59,6,0 K03455 2599 . A <*> 0 . END=2603 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 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 K03455 2607 . A <*> 0 . END=2607 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 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 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 K03455 2610 . G <*> 0 . END=2612 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 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 K03455 2614 . A <*> 0 . END=2614 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 K03455 2615 . A <*> 0 . END=2615 GT:GQ:MIN_DP:PL 0/0:15:5:0,15,149 K03455 2616 . C <*> 0 . END=2616 GT:GQ:MIN_DP:PL ./.:0:7:8,0,158 K03455 2617 . A <*> 0 . END=2617 GT:GQ:MIN_DP:PL ./.:0:6:11,0,131 K03455 2618 . A <*> 0 . END=2618 GT:GQ:MIN_DP:PL 0/0:18:6:0,18,179 K03455 2619 . T <*> 0 . END=2619 GT:GQ:MIN_DP:PL 0/0:21:7:0,21,209 K03455 2620 . G <*> 0 . END=2620 GT:GQ:MIN_DP:PL 0/0:39:13:0,39,389 K03455 2621 . G <*> 0 . END=2651 GT:GQ:MIN_DP:PL 0/0:50:49:0,147,1469 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 K03455 2653 . T <*> 0 . END=2659 GT:GQ:MIN_DP:PL 0/0:50:201:0,300,2999 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 K03455 2661 . T <*> 0 . END=2663 GT:GQ:MIN_DP:PL 0/0:50:213:0,300,2999 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 K03455 2665 . C <*> 0 . END=2668 GT:GQ:MIN_DP:PL 0/0:50:240:0,300,2999 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