Hello!
I am trying to run Parabricks HaplotypeCaller in genotype-only mode. I.e., i have a set of sites from two parents sequenced at 60x coverage, and I would like to genotype offspring sequenced at 10x from those parents only at those pre-selected sites, without doing variant discovery.
In standard gatk HaplotypeCaller this is achieved with —alleles and --gt-mode GENOTYPE_GIVEN_ALLELES options (or similar depending on version).
I was wondering how/if I can achieve the same behaviour with the Parabricks implementation of HaplotypeCaller.
I see there is the —htvc-alleles flag. Would using this achieve the same desired behaviour (i.e., genotype only at a set of golden true sites.
Any help would be appreciated as currently the documentation was not enough to resolve this query,
Kind regards,
Lorenzo