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Two types of separators for GT in vcf file

HaseungHaseung Republic of KoreaMember

Hi,
I've tried joint genotyping process with 'GenotypeGVCFs' tool in GATK v4.1.2 and the output has generated without any errors. However, there is something weird that I couldn't understand. In the vcf file, there exists two types of GT separator, '|' and '/'.

1   38  .   C   CA  10745.24    .   AC=92;AF=0.920;AN=100;DP=210;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4128;MLEAC=106;MLEAF=1.00;MQ=36.67;QD=25.36;SOR=10.626 GT:AD:DP:GQ:PGT:PID:PL:PS   1|1:0,19:19:69:1|1:38_C_CA:996,69,0:38  1|1:0,1:1:6:1|1:38_C_CA:81,6,0:38   1|1:0,24:24:75:1|1:38_C_CA:1110,75,0:38 1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,19:19:63:1|1:38_C_CA:926,63,0:38  1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,5:5:18:1|1:38_C_CA:261,18,0:38    1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,2:2:9:1|1:38_C_CA:126,9,0:38  1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,3:3:12:1|1:38_C_CA:171,12,0:38    1|1:0,1:1:6:1|1:38_C_CA:90,6,0:38   1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    0/0:1,0:1:3:.:.:0,3,28  1|1:0,6:6:18:1|1:38_C_CA:270,18,0:38    ./.:2,0:2:.:.:.:0,0,./.:0,0:0:.:.:.:0,0,0   1|1:0,4:4:18:1|1:38_C_CA:261,18,0:38    ./.:0,0:0:.:.:.:0,0,0   1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   ./.:0,0:0:.:.:.:0,0,1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,3:3:12:1|1:38_C_CA:171,12,0:38    1|1:0,5:5:15:1|1:38_C_CA:225,15,0:38    1|1:0,1:1:6:1|1:38_C_CA:90,6,0:38   ./.:0,0:0:.:.:.:0,0,0   1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,5:5:15:1|1:38_C_CA:225,15,0:38    1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   ./.:2,0:2:.:.:.:0,0,0   1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  0/0:1,0:1:3:.:.:0,3,34  ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,35  1|1:0,5:5:15:1|1:38_C_CA:225,15,0:38    1|1:0,5:5:18:1|1:38_C_CA:270,18,0:38    1|1:0,6:6:18:1|1:38_C_CA:270,18,0:38    1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  0/0:1,0:1:3:.:.:0,3,34  1|1:0,2:2:6:1|1:38_C_CA:90,6,0:38   1|1:0,3:3:12:1|1:38_C_CA:171,12,0:38    1|1:0,3:3:9:1|1:38_C_CA:135,9,0:38  1|1:0,5:5:21:1|1:38_C_CA:306,21,0:38    1|1:0,1:1:6:1|1:38_C_CA:90,6,0:38   1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38    1|1:0,5:5:15:1|1:38_C_CA:225,15,0:38    1|1:0,4:4:12:1|1:38_C_CA:180,12,0:38

I couldn't find any options that correct this situation in the tool documentations.
Looking forward to your reply. Thank you!

Answers

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