This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Phasing with HC
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?