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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Is FMT/PL supported by slivar? #173

Closed weizhu365 closed 1 week ago

weizhu365 commented 1 week ago

I noticed that GQ is not so good compared to FMT/PL. I would like to use:

kid.PL[3]==0 && kid.PL[1]>20 && kid.PL[2]>20

rather than "kid.het" in slivar filtering.

But I got 0 variant after filtering. I would like to know whether PL is supported in a way like "AD" in slivar.

If not, is it possible to add "PL" support to slivar?

Thanks,

Wei Zhu

brentp commented 1 week ago

It should be supported. I think you'd want to use only:

kid.PL[3] < 1 && kid.PL[1]>20 && kid.PL[2] < 1

since you're wanting the het genotype high probability. or you can do:

kid.PL[3]==0 && (kid.PL[1]>20 || kid.PL[2]>20)
weizhu365 commented 1 week ago

Thanks for your quick reply and it is working now,

best,

Wei