Hello
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 ?
↧
HaplotypeCaller on sliced BAMs
↧
