Speeding up HaplotypeCaller analysis

Speeding up HaplotypeCaller analysis

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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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