Genotypes in vcf files
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3 months ago
amy__ ▴ 160

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

genotypes vcf • 697 views
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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!

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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
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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!

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3 months ago

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

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

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