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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!