GT field in VCF only has one number?

Question

[DVA]

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.

Answer 1

[chrchang523]

Some ways for this to happen:

1. While females have two copies of each of the first 23 chromosomes, males have only one copy of chrX and one copy of chrY; in those cases, you'd only expect to see a single number.
2. A single number is also common for mitochondrial DNA.
3. Suppose you have a large deletion on one copy of another chromosome. If this SNP overlaps such a deletion, some software will report your genotype as a single number (though the latest VCF standard recommends a '*' allele code to represent the middle of a deletion).

This looks like case #3, since rs2682358 is on chromosome 1.

[DVA]

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...

[DVA]

By the way, would you please comment on why the software did not take the line3 and line2 as one single indel case?