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Symbolic alleles returned when --types ref requested

Open pd3 opened this issue 3 years ago • 0 comments

Because the unseen star allele is not supported by bcf_get_variant_types, the command bcftools view --types ref is unable to distinguish between the star allele and other symbolic alleles, such as <CNV>, <INS>, etc. This could be fixed either in bcftools or in bcftools+extend htslib API.

See https://github.com/samtools/htslib/pull/1467#issuecomment-1186930979 and https://github.com/samtools/htslib/pull/1467#issuecomment-1190006133

pd3 avatar Jul 20 '22 08:07 pd3