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.
Speed up HaplotypeCaller
I am trying performed a HaplotypeCaller in pool samples. However, it's taking a very long time (more than 72h).
I am using this command:
java -XX:ParallelGCThreads=15 -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R genome.fa -I $dir_in/$fw.split.bam -dontUseSoftClippedBases -stand_call_conf 20.0 --ploidy 20 -o $dir_out/$fw.vcf
Have any way to optimize this process?Any suggestion will be appreciated!