bcftools
bcftools copied to clipboard
Symbolic alleles returned when --types ref requested
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