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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 7 months ago

krukanna commented 7 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 7 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 !)