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speeding up HaplotyperCaller
I've started to call variants on 200 diploid individuals with a genome size of 160Mb, using HaplotypeCaller and 20 cores. In about 10 hours it's covered the first 600,000 bases, so it looks like completion will take several months. I could potentially use up to 64 cores although this would inhibit other users.
My input parameters are as below. They are probably pretty loose. I plan on hard-filtering variants after this.
Do you have any advice on how to speed this up?
--heterozygosity 0.01 \ --indel_heterozygosity 0.001 \ -stand_call_conf 31 \ -stand_emit_conf 31 \ -mbq 10 \ -gt_mode DISCOVERY \ -L chr2L -L chr2R -L chr3L -L chr3R -L chrX -L chr4 -L chrM \