If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GenotypeGVCFs multithread not working properly

Hi GATK team,
I ran the haplotypcaller on a single mapped bam file. Command:

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I MyMappedSample.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o MyMappedSample.g.vcf -L hg38.exome.regions.bed

From this output, I am running the GenotypeGVCFs. Command:

java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R Homo_sapiens_assembly38.fasta --variant MyMappedSample.g.vcf -o MyMappedSample.geontyped.vcf -nt 32 -L hg38.exome.regions.bed

The issue that I am is that when running the GenotypeGVCFs, even though I have the "-nt" flag, it is not using multiple threads, and only running with a single thread. I am only running this on a single sample. I am using version 3.5 (we have not yet updated our system to a java 8). Is this an issue with version 3.5, and I should maybe try an earlier version?

Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    This is unlikely to be a GATK problem; it's more likely that your system does not support multithreading or does not have access to multiple cores. Multithreading does work automatically on all systems.

  • elondinelondin Member

    Thank you for your response. Our system does support multithreading. It seems that it is just this 1 module of GATK that doesn't work with the multithreading. Everything else that can use a multithread does work (including other non-GATK applications). Oddly, when I add the "-nt" flag it tells me that it will take ~5hrs to finish, but without this flag it will finish it ~5 min...Not sure what it going on here.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Have a look at Geraldine's response in this thread from February 25th.


Sign In or Register to comment.