We've moved!
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!

HaplotypeCaller on sliced BAMs

I'm trying to do germline calling using HaplotypeCaller. However, I'm only interested in obtaining germline variants for a subset of the genome. To save space and compute resources, I was hoping to use a sliced BAM that includes reads spanning only my regions of interest. Can HaplotypeCaller handle such sliced BAM files and correctly infer germline SNPs for those regions ?

Best Answer


Sign In or Register to comment.