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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Select inherited variants #160

Open krukanna opened 11 months ago

krukanna commented 11 months ago

Hello, Is it possible to select only variants that are definitely inherited from parents, also taking into account alleles? I tried with function below to control genotypes. But that function don't care for alleles, only genotypes. --trio "inherited:(mom.het && dad.het && kid.het) || (mom.hom_ref && dad.het && kid.het) || (mom.het && dad.hom_ref && kid.het) || (mom.het && dad.het && kid.hom_alt) || (mom.hom_alt && dad.hom_alt && kid.hom_alt) || (mom.hom_alt && dad.het && kid.hom_alt) || (mom.het && dad.hom_alt && kid.hom_alt)"

I found some cases with multialleles variants, for example: ref: CA alt: C,CAA GT: mom: 0/1, dad: 0/1, kid: 0/2 So it should be classified as de novo deletion not inherited variant.

Do you have maybe better solution? Thanks.

brentp commented 11 months ago

Hi, slivar will give a warning about multiple alleles. You should decompose your VCF before using with slivar.

You expression otherwise is, I think fine, but it might be easier to enumerate the non-inherited variants and then negate that expression (with !)