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setGT problem with phased genotypes #1844

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VLoegler opened this issue Jan 6, 2023 · 1 comment
Closed

setGT problem with phased genotypes #1844

VLoegler opened this issue Jan 6, 2023 · 1 comment

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@VLoegler
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VLoegler commented Jan 6, 2023

Hi,

I'm using setGT to change half missing genotypes (./1) to fully missing genotypes. The problem is that I have some phased genotypes (ex: 0|. 2|.) and setGT doesn't handle these one.

Here is the command I used:

bcftools +setGT -- -t ./x -n .

The possibility to have -t .|x would be very useful.
@pd3 pd3 closed this as completed in dfdb092 Jan 13, 2023
@pd3
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pd3 commented Jan 13, 2023 •
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The usage page suggests that both phased and unphased half-missing genotypes are supported

./x  .. partially missing (e.g., "./0" or ".|1" but not "./.")

however, it turns out that was not the case.

The bug is now fixed, thanks for reporting the issue.

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@pd3 @VLoegler