Genotypes in vcf files

Question

[amy__]

Hi all,

I have a variety of genotypes outputted in my vcf, these being:

0 1 0/0 0/1 1/1 1/2

Now I can assume these ones:

0 1 0/0 = homozygous for the reference 0/1 = heterozygous for the alternate 1/1 = homozygous for the alternate 1/2 = heterozygous with two reference options

But the 0 and 1 have me stumped - I assume 1 is to do with the alternate being present but I cannot find anything online about it.

Thanks! Amy

[Pierre Lindenbaum]

but I cannot find anything online about it.

1/2 in VCF genotype field? ; Genotype representation with 0, 1, 2 - what do they mean? ; Meaning Of Genotype 2/0 And 2/1 ; Understanding 1/1 output in VCF ; What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent? ; GT 2/3, or 3/3 or 2/2 in vcf

[amy__]

Yes I am aware, the only one of those posts which relates to a single 1 or a single 0 being outputted is the Genotype representation with 0, 1, 2 - what do they mean? - which just states that those regions may be haploid or deletions in that region? Would that be a region that is covered by a CNV deletion or insertion? Apart from that post, I cannot find any official pages that describe exactly what it means. Would these technically be similar to that of a hemizygous variant? Thanks!

[Pierre Lindenbaum]

Would that be a region that is covered by a CNV deletion or insertion?

something like:

##ALT=<ID=CNV,Description="Copy number variant region">
(...)
chr1 12345 . A <CNV> . . SVLEN=1000;END=13345 GT 0/1

[amy__]

Thanks! So I did not do CNV calling with these, so I think it is unlikely to be from that - these were called using the starling (Isaac variant caller). I will email Illumina and see what they say. Thanks!

Answer 1

[Jeremy Leipzig]

if the 0 or 1 stands alone it is just a hemizygous call such as those on chrX or chrY in males

[amy__]

Oh amazing, thank you! I will check the sex and assume you are correct. Thank you lots!