The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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 ?