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Speeding up HaplotypeCaller analysis

how can I speed up the HaplotypeCaller command running?

input bam file is about 16G and running time using the below command is about 15 hours.

java -Xmx64G -jar GenomeAnalysisTK.jar -nt 1 -nct 34 -T HaplotypeCaller -R Renamed.fasta -I realigned.bam -o raw_variants.g.vcf.gz -ERC GVCF

GATK version: 3.7

CPU: 2.2 * 48

RAM: 251G

linux cpu haplotypecaller
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by kk.mahsa kk.mahsa

I think you should consider this command for Haplotypecaller analysis:

gatk --java-options "-Xmx64g" HaplotypeCaller -R Renamed.fasta -I realigned.bam -O raw_variants.g.vcf.gz -ERC GVCF
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written by tothepoint tothepoint

Thanks for trying to help but please pay attention to the question before answering. My GATK version is 3.7 not 4. The issue of HaplotypeCaller analysis is about the CPU, not the RAM.

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written by kk.mahsa kk.mahsa

Indeed I missed GATK version. The only way I found to speed up haplotypecaller in earlier version of GATK is to increase -nct flag.

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written by tothepoint tothepoint

how can I speed up the HaplotypeCaller command running?

run in parallel, for each chromosome

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written by Pierre Lindenbaum Pierre Lindenbaum

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