Entering edit mode
6.7 years ago
DVA
▴
630
I recently got some VCF files from Illumina (IVC output), and I noticed that there are certain lines having GT field only with 1 number. For example, see the 3rd line below (I'm including the adjacent lines.):
chr1 21723729 . T C 123.0 PASS SNVSB=-17.2;SNVHPOL=4;EFF=INTERGENIC(MODIFIER||||||||||1);dbSNP138_ID=rs2176878;dbSNP142_ID=rs2176878;1000G_phase1_release_v3_AF=0.45 GT:GQ:GQX:DP:DPF:AD 0/1:156:123:19:1:11,8
chr1 21723798 . TTA T 281.0 PASS CIGAR=1M2D;RU=TA;REFREP=1;IDREP=0;EFF=INTERGENIC(MODIFIER||||||||||1);dbSNP138_ID=rs202144135;dbSNP142_ID=rs202144135;1000G_phase1_release_v3_AF=0.48 GT:GQ:GQX:DPI:AD 0/1:321:281:19:12,7
#######################see this line below, INFO column with GT is at the end of the line########################
chr1 21723800 . A T 221.0 PASS SNVSB=-22.2;SNVHPOL=15;EFF=INTERGENIC(MODIFIER||||||||||1);dbSNP138_ID=rs2682358;dbSNP142_ID=rs2682358 GT:GQ:GQX:DP:DPF:AD 1:30:30:11:0:0,11
chr1 21724072 . G C 163.0 PASS SNVSB=-18.9;SNVHPOL=2;EFF=INTERGENIC(MODIFIER||||||||||1);dbSNP138_ID=rs1568407;dbSNP142_ID=rs1568407;1000G_phase1_release_v3_AF=0.52 GT:GQ:GQX:DP:DPF:AD 0/1:163:160:19:1:8,11
(I find this in almost all chromosomes. This sample is from a healthy tissue.)
I'm expecting to only see things like 0/1, 1/1, 1/2... and have never seen one single number before. Any idea what does it mean please? (Cases like line3 are only a portion of my file).
Thank you.
Thank you so much for the reply. Great points! I added some adjacent lines from the original file, and interestingly all the "1" GT cases are next to a indel case. I wonder why IVC did not put line3 with line2 as an indel case...
By the way, would you please comment on why the software did not take the line3 and line2 as one single indel case?