Haplotypecaller taking too long
When I run the pipeline according to best practices, HC on a fastq of 60MB (for a targeted panel) takes about 10 minutes, but then for the same pipeline/targeted region, on a fastq of 150MB, HC takes 6 hrs. Any idea what would explain such a stark jump in runtime? Also, is there any way to reduce it? Can I use -Xmx -Xms arguments to increase the speed if memory is not an issue?
Any help will be appreciated.