a b/deeptrio/testdata/golden.training_examples.vcf 

  1
  
##fileformat=VCFv4.2





  
  

  2
  
##FILTER=<ID=PASS,Description="All filters passed">





  
  

  3
  
##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference.">





  
  

  4
  
##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">





  
  

  5
  
##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call.">





  
  

  6
  
##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)">





  
  

  7
  
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">





  
  

  8
  
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">





  
  

  9
  
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">





  
  

  10
  
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block.">





  
  

  11
  
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">





  
  

  12
  
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">





  
  

  13
  
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">





  
  

  14
  
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">





  
  

  15
  
##DeepVariant_version=1.8.0





  
  

  16
  
##contig=<ID=20,length=63025520>





  
  

  17
  
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  child





  
  

  18
  
20  10001019    .   T   G   0   .   .   GT:DP:AD:VAF    0/1:16:10,6:0.375





  
  

  19
  
20  10001298    .   T   A   0   .   .   GT:DP:AD:VAF    1/1:23:0,23:1





  
  

  20
  
20  10001436    .   A   AAGGCT  0   .   .   GT:DP:AD:VAF    1/1:25:0,23:0.92





  
  

  21
  
20  10001474    .   C   T   0   .   .   GT:DP:AD:VAF    1/1:22:0,22:1





  
  

  22
  
20  10001617    .   C   A   0   .   .   GT:DP:AD:VAF    0/1:18:11,7:0.388889





  
  

  23
  
20  10001628    .   G   A   0   .   .   GT:DP:AD:VAF    1/1:20:0,20:1





  
  

  24
  
20  10001661    .   T   C   0   .   .   GT:DP:AD:VAF    1/1:16:0,16:1





  
  

  25
  
20  10001670    .   T   G   0   .   .   GT:DP:AD:VAF    1/1:18:0,18:1





  
  

  26
  
20  10002058    .   T   G   0   .   .   GT:DP:AD:VAF    1/1:18:0,18:1





  
  

  27
  
20  10002099    .   C   T   0   .   .   GT:DP:AD:VAF    0/1:17:6,11:0.647059





  
  

  28
  
20  10002138    .   C   G   0   .   .   GT:DP:AD:VAF    1/1:15:0,15:1





  
  

  29
  
20  10002142    .   G   C   0   .   .   GT:DP:AD:VAF    1/1:15:0,13:0.866667





  
  

  30
  
20  10002625    .   G   T   0   .   .   GT:DP:AD:VAF    1/1:22:0,22:1





  
  

  31
  
20  10003021    .   C   T   0   .   .   GT:DP:AD:VAF    1/1:17:0,17:1





  
  

  32
  
20  10003358    .   A   C   0   .   .   GT:DP:AD:VAF    0/1:16:12,4:0.25





  
  

  33
  
20  10003651    .   T   C   0   .   .   GT:DP:AD:VAF    1/1:16:0,16:1





  
  

  34
  
20  10003692    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:13:0,13:1





  
  

  35
  
20  10003832    .   G   A   0   .   .   GT:DP:AD:VAF    1/1:27:0,27:1





  
  

  36
  
20  10004094    .   A   C   0   .   .   GT:DP:AD:VAF    1/1:13:0,13:1





  
  

  37
  
20  10004114    .   C   G   0   .   .   GT:DP:AD:VAF    0/0:15:13,2:0.133333





  
  

  38
  
20  10004128    .   AG  A   0   .   .   GT:DP:AD:VAF    0/0:18:15,2:0.111111





  
  

  39
  
20  10004147    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:15:0,15:1





  
  

  40
  
20  10004351    .   C   G   0   .   .   GT:DP:AD:VAF    1/1:20:0,20:1





  
  

  41
  
20  10004389    .   T   G   0   .   .   GT:DP:AD:VAF    1/1:22:0,22:1





  
  

  42
  
20  10004610    .   A   C   0   .   .   GT:DP:AD:VAF    1/1:18:0,18:1





  
  

  43
  
20  10004725    .   A   G   0   .   .   GT:DP:AD:VAF    0/1:21:7,14:0.666667





  
  

  44
  
20  10004769    .   TAAAACTATGC T   0   .   .   GT:DP:AD:VAF    0/1:22:8,14:0.636364





  
  

  45
  
20  10004874    .   A   C   0   .   .   GT:DP:AD:VAF    1/1:32:0,32:1





  
  

  46
  
20  10004887    .   A   G   0   .   .   GT:DP:AD:VAF    0/1:30:16,14:0.466667





  
  

  47
  
20  10005010    .   C   T   0   .   .   GT:DP:AD:VAF    1/1:25:0,25:1





  
  

  48
  
20  10005427    .   C   T   0   .   .   GT:DP:AD:VAF    1/1:20:0,20:1





  
  

  49
  
20  10005499    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:25:0,25:1





  
  

  50
  
20  10005587    .   A   G   0   .   .   GT:DP:AD:VAF    0/1:34:20,14:0.411765





  
  

  51
  
20  10005723    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:32:0,32:1





  
  

  52
  
20  10006291    .   G   A   0   .   .   GT:DP:AD:VAF    0/1:29:17,12:0.413793





  
  

  53
  
20  10006682    .   T   A   0   .   .   GT:DP:AD:VAF    1/1:23:0,23:1





  
  

  54
  
20  10006819    .   AAAAC   A   0   .   .   GT:DP:AD:VAF    1/1:25:0,25:1





  
  

  55
  
20  10007150    .   G   C   0   .   .   GT:DP:AD:VAF    0/1:32:13,19:0.59375





  
  

  56
  
20  10007175    .   C   T   0   .   .   GT:DP:AD:VAF    0/1:33:17,16:0.484848





  
  

  57
  
20  10007352    .   C   T   0   .   .   GT:DP:AD:VAF    1/1:26:0,26:1





  
  

  58
  
20  10007531    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:21:0,21:1





  
  

  59
  
20  10007980    .   A   C   0   .   .   GT:DP:AD:VAF    1/1:21:1,20:0.952381





  
  

  60
  
20  10008146    .   TA  T   0   .   .   GT:DP:AD:VAF    1/1:29:1,27:0.931035





  
  

  61
  
20  10008221    .   T   C   0   .   .   GT:DP:AD:VAF    1/1:24:1,23:0.958333





  
  

  62
  
20  10008458    .   T   G   0   .   .   GT:DP:AD:VAF    1/1:26:0,26:1





  
  

  63
  
20  10009227    .   A   G   0   .   .   GT:DP:AD:VAF    0/1:31:14,17:0.548387





  
  

  64
  
20  10009246    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:35:0,35:1





  
  

  65
  
20  10009400    .   T   A   0   .   .   GT:DP:AD:VAF    1/1:33:0,32:0.969697





  
  

  66
  
20  10009512    .   C   G   0   .   .   GT:DP:AD:VAF    1/1:26:0,26:1





  
  

  67
  
20  10009719    .   A   G   0   .   .   GT:DP:AD:VAF    1/1:19:0,18:0.947368