MCHap can report haplotypes that have not been called in the posterior mode of any individual (i.e., and allele count of 0). This is necessary when reporting statistics over the posterior (such as the posterior mean allele frequencies) but is not needed if we just want genotype calls. It would be nice to have an option to exclude uncalled alleles from the output VCF file. E.g. a simple flag like --drop-uncalled-haplotypes. This could potentially raise an error if used combination with an option to report posterior summary stats.
timothymillar
commented
1 year ago
MCHap can report haplotypes that have not been called in the posterior mode of any individual (i.e., and allele count of 0). This is necessary when reporting statistics over the posterior (such as the posterior mean allele frequencies) but is not needed if we just want genotype calls. It would be nice to have an option to exclude uncalled alleles from the output VCF file. E.g. a simple flag like
--drop-uncalled-haplotypes. This could potentially raise an error if used combination with an option to report posterior summary stats.