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What is the correct syntax for intervals for multiple chromosomes using the -L flag


I've previously defined intervals using the -L flag with HaplotypeCaller for say -L chr1 for chromosome 1, and -L chr1 and -L chr2 for chromosome 1 and chromosome 2. What is the syntax for putting this both into the same interval?

I was trying to follow the idea in Table 2 in Performance benchmarking of GATK3.8 and GATK4, DOI:10.1101/348565 of Chunking of the genome by chromosomes, but I couldn't follow the documentation here: software.broadinstitute.org/gatk/documentation/article?id=4133 as to how to actually do that.

Many thanks,



  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @AlistairB

    You can use it is this way: -L chr1,chr2

  • AlistairBAlistairB Member
    Hi Bhanu,

    Thank you for your reply. I'm pretty sure I tried comma separation, as well as tabs, colons, semi-colons, spaces and brackets, but I'll try it again when the current job has finished. I forgot to say that I'm using the latest docker container to run GATK. And I've been trying to follow the GATK Best Practices.

    My follow up question would be - and I've only started using GATK this year - is that I come across several gaps in the documentation so far, such as the change to VariantRecalibrator from --resource hapmap, to --resource:hapmap,, and was wondering if community members are able to contribute to updating the documentation somehow?

    All the best,

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @AlistairB

    Can you please point me to the VariantRecalibrator doc you are reffering to.

  • AlistairBAlistairB Member
    Ah, I think it's my mistake. I must have accidentally strayed into the beta documentation via Google instead of going through the sidebar on the GATK site:

    I'm not allowed to post links, but the end of the path is: documentation/tooldocs/4.beta.4/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php
  • shatha92shatha92 Member
    Hi Alistair,
    I was struggling like you until I found a solution, try running the command with -L chr1 -L chr2...
    thanks to Ms Sheila.
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