Speeding up HaplotypeCaller analysis
0
0
Entering edit mode
6 weeks ago
kk.mahsa ▴ 140

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 • 277 views
ADD COMMENT
1
Entering edit mode

how can I speed up the HaplotypeCaller command running?

run in parallel, for each chromosome

ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thank you

ADD REPLY

Login before adding your answer.

Traffic: 1432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6