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/deeptrio/testdata/golden.training_examples.vcf
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| a | b/deeptrio/testdata/golden.training_examples.vcf | ||
|---|---|---|---|
| 1 | ##fileformat=VCFv4.2 |
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| 2 | ##FILTER=<ID=PASS,Description="All filters passed"> |
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| 3 | ##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference."> |
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| 4 | ##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold."> |
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| 5 | ##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call."> |
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| 6 | ##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)"> |
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| 7 | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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| 8 | ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> |
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| 9 | ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> |
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| 10 | ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block."> |
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| 11 | ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> |
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| 12 | ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions."> |
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| 13 | ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer"> |
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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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| 15 | ##DeepVariant_version=1.8.0 |
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| 16 | ##contig=<ID=20,length=63025520> |
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| 17 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child |
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| 18 | 20 10001019 . T G 0 . . GT:DP:AD:VAF 0/1:16:10,6:0.375 |
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| 19 | 20 10001298 . T A 0 . . GT:DP:AD:VAF 1/1:23:0,23:1 |
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| 20 | 20 10001436 . A AAGGCT 0 . . GT:DP:AD:VAF 1/1:25:0,23:0.92 |
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| 21 | 20 10001474 . C T 0 . . GT:DP:AD:VAF 1/1:22:0,22:1 |
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| 22 | 20 10001617 . C A 0 . . GT:DP:AD:VAF 0/1:18:11,7:0.388889 |
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| 23 | 20 10001628 . G A 0 . . GT:DP:AD:VAF 1/1:20:0,20:1 |
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| 24 | 20 10001661 . T C 0 . . GT:DP:AD:VAF 1/1:16:0,16:1 |
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| 25 | 20 10001670 . T G 0 . . GT:DP:AD:VAF 1/1:18:0,18:1 |
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| 26 | 20 10002058 . T G 0 . . GT:DP:AD:VAF 1/1:18:0,18:1 |
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| 27 | 20 10002099 . C T 0 . . GT:DP:AD:VAF 0/1:17:6,11:0.647059 |
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| 28 | 20 10002138 . C G 0 . . GT:DP:AD:VAF 1/1:15:0,15:1 |
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| 29 | 20 10002142 . G C 0 . . GT:DP:AD:VAF 1/1:15:0,13:0.866667 |
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| 30 | 20 10002625 . G T 0 . . GT:DP:AD:VAF 1/1:22:0,22:1 |
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| 31 | 20 10003021 . C T 0 . . GT:DP:AD:VAF 1/1:17:0,17:1 |
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| 32 | 20 10003358 . A C 0 . . GT:DP:AD:VAF 0/1:16:12,4:0.25 |
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| 33 | 20 10003651 . T C 0 . . GT:DP:AD:VAF 1/1:16:0,16:1 |
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| 34 | 20 10003692 . A G 0 . . GT:DP:AD:VAF 1/1:13:0,13:1 |
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| 35 | 20 10003832 . G A 0 . . GT:DP:AD:VAF 1/1:27:0,27:1 |
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| 36 | 20 10004094 . A C 0 . . GT:DP:AD:VAF 1/1:13:0,13:1 |
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| 37 | 20 10004114 . C G 0 . . GT:DP:AD:VAF 0/0:15:13,2:0.133333 |
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| 38 | 20 10004128 . AG A 0 . . GT:DP:AD:VAF 0/0:18:15,2:0.111111 |
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| 39 | 20 10004147 . A G 0 . . GT:DP:AD:VAF 1/1:15:0,15:1 |
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| 40 | 20 10004351 . C G 0 . . GT:DP:AD:VAF 1/1:20:0,20:1 |
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| 41 | 20 10004389 . T G 0 . . GT:DP:AD:VAF 1/1:22:0,22:1 |
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| 42 | 20 10004610 . A C 0 . . GT:DP:AD:VAF 1/1:18:0,18:1 |
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| 43 | 20 10004725 . A G 0 . . GT:DP:AD:VAF 0/1:21:7,14:0.666667 |
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| 44 | 20 10004769 . TAAAACTATGC T 0 . . GT:DP:AD:VAF 0/1:22:8,14:0.636364 |
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| 45 | 20 10004874 . A C 0 . . GT:DP:AD:VAF 1/1:32:0,32:1 |
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| 46 | 20 10004887 . A G 0 . . GT:DP:AD:VAF 0/1:30:16,14:0.466667 |
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| 47 | 20 10005010 . C T 0 . . GT:DP:AD:VAF 1/1:25:0,25:1 |
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| 48 | 20 10005427 . C T 0 . . GT:DP:AD:VAF 1/1:20:0,20:1 |
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| 49 | 20 10005499 . A G 0 . . GT:DP:AD:VAF 1/1:25:0,25:1 |
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| 50 | 20 10005587 . A G 0 . . GT:DP:AD:VAF 0/1:34:20,14:0.411765 |
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| 51 | 20 10005723 . A G 0 . . GT:DP:AD:VAF 1/1:32:0,32:1 |
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| 52 | 20 10006291 . G A 0 . . GT:DP:AD:VAF 0/1:29:17,12:0.413793 |
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| 53 | 20 10006682 . T A 0 . . GT:DP:AD:VAF 1/1:23:0,23:1 |
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| 54 | 20 10006819 . AAAAC A 0 . . GT:DP:AD:VAF 1/1:25:0,25:1 |
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| 55 | 20 10007150 . G C 0 . . GT:DP:AD:VAF 0/1:32:13,19:0.59375 |
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| 56 | 20 10007175 . C T 0 . . GT:DP:AD:VAF 0/1:33:17,16:0.484848 |
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| 57 | 20 10007352 . C T 0 . . GT:DP:AD:VAF 1/1:26:0,26:1 |
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| 58 | 20 10007531 . A G 0 . . GT:DP:AD:VAF 1/1:21:0,21:1 |
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| 59 | 20 10007980 . A C 0 . . GT:DP:AD:VAF 1/1:21:1,20:0.952381 |
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| 60 | 20 10008146 . TA T 0 . . GT:DP:AD:VAF 1/1:29:1,27:0.931035 |
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| 61 | 20 10008221 . T C 0 . . GT:DP:AD:VAF 1/1:24:1,23:0.958333 |
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| 62 | 20 10008458 . T G 0 . . GT:DP:AD:VAF 1/1:26:0,26:1 |
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| 63 | 20 10009227 . A G 0 . . GT:DP:AD:VAF 0/1:31:14,17:0.548387 |
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| 64 | 20 10009246 . A G 0 . . GT:DP:AD:VAF 1/1:35:0,35:1 |
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| 65 | 20 10009400 . T A 0 . . GT:DP:AD:VAF 1/1:33:0,32:0.969697 |
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| 66 | 20 10009512 . C G 0 . . GT:DP:AD:VAF 1/1:26:0,26:1 |
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| 67 | 20 10009719 . A G 0 . . GT:DP:AD:VAF 1/1:19:0,18:0.947368 |