This adds two command line options to find sites:
--AN-field
--AF-field
which allow the selection of the AN and AF field in the INFO column of the vcf. This is useful, because gnomad, for example, has population specific AF/AN fields. The default behaviour is unchanged.
This adds two command line options to find sites: --AN-field --AF-field which allow the selection of the AN and AF field in the INFO column of the vcf. This is useful, because gnomad, for example, has population specific AF/AN fields. The default behaviour is unchanged.
Unrelated, but I am also wondering, why select-sites excludes variants with a Cytosine in ref on autosomes, see https://github.com/brentp/somalier/blob/master/src/somalierpkg/findsites.nim#L135