HaplotypeCaller is slow
My variant calling seems very slow. What do you think?
We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB.
I am using the HaplotypeCaller with 8 threads (-nct 8) and it is taking 31 hours.
When we start whole genome sequencing this will be impossible!
Any ideas on how to speed things up? Is this a normal speed?