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Feature request: --new-gt c:0/X #2065

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pd3 opened this issue Dec 30, 2023 · 0 comments

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pd3 commented Dec 30, 2023

+setGT does not allow the use of X in custom genotypes, eg --new-gt c:'0/M' is acceptable, but c:'0/X' causes the following error:

Could not parse the genotype: c:0/X

Could this capability be added?

Originally posted by @JosephLalli in #1800 (comment)

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pd3 mentioned this issue

bcftools +setGT does not consider major allele as new genotype #1800

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