how can i set num of cores when use haplotypecaller

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xuekai yang

• December 17, 2020 06:55
• Edited

version: 4.1.9.0

my command: gatk --java-options "-Xmx16G" HaplotypeCaller -I bam -R fasta -mbq 20 -O vcf.gz

 

which option can setting the function?

I can`t find this option by too many option of HaplotypeCaller.

Thanks.

 

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  woodword

  • December 28, 2020 10:04

  Some of GATK tools use multi-threads, but most don't. Usually user should split their interval files and process each of them simultaneously to speed up. Once all intervals are finished, one can merge the results as the final one.

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  xuekai yang

  • January 07, 2021 02:54

  hi , woodword, that a good idea.

  sorry, I just saw it.  I chose haplotypecallerSpark to callvariant, it can also solve my problem.

  Thanks for replying.

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  Bhanu Gandham

  • January 08, 2021 20:14

  woodword Thank you so much for jumping in and helping the GATK community by contributing to the information we provide to the community through this forum!!

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