Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 \