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Phasing with HC

skhalid7skhalid7 GatechMember

I'm currently calling variants using HaplotypeCaller on different subsections of a WGS file (<5Mbp). The number of phased variants that show up are very low. How can I increase the 'yield' of phased genotypes? Will running HC on the entire WGS sample instead of chunks help?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    What do you mean by "different subsections"? Have a look at this thread.


  • skhalid7skhalid7 GatechMember

    Currently I'm extracting genes of interest and then running haplotype caller on them. The number of phased sites that come up are very few. Will running HC on the entire chromosome or genome yield more phased sites or will it not make much of a difference?

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