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Need to include custom interval list in gatk/processing-for-variant-discovery-gatk4

dannykwellsdannykwells San FranciscoMember ✭✭

Not sure if this is a GATK question or Firecloud question, but:

According to this article, it is recommended that a set of intervals be used with BQSR when working with exomes. However, in the best practices pipelines that is posted on firecloud here made by @bshifaw does not include any clear way to directly use a more targeted interval list, and appears to actually just scatter over chromosomes (and this pipeline explicitly mentions that it can be used with WES data). In theory I'm fine with this but I wanted to ask - how important is it to use a set of intervals with BQSR for WES data? Is it ok to leave this as is, or should I include an interval list?

Issue · Github
by bshifaw

Issue Number
Last Updated
Closed By


  • bshifawbshifaw Member, Broadie, Moderator admin
    edited August 2018

    Hey @dannykwells
    This is a GATK question, I'll have to refer to the dev team on the importance of using set intervals for BQSR.

    Post edited by bshifaw on
  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Thank you Beri for beginning the conversation with the dev team. As this is more related to GATK, I'm moving it to the appropriate forum. There is no further action needed on your part @dannykwells at this point, I just want to make sure the right people keep track of this thread going forward.

  • dannykwellsdannykwells San FranciscoMember ✭✭

    Ok cool - The link to the issue above did not work (for me) - maybe it's an internal Broad link? Anyway, let me know. Thanks!!

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited August 2018

    I contacted the dev team, their advice is to follow the articles suggestion when working with exome data, you’ll need to edit the workflow to handle exomes like editing the BQSR intervals you mentioned. There is a workflow being developed specifically for exome processing, we’ll make this available in the near future.
    We'll make the approriate changes to remove that bit about exomes in the WDL to avoid confusing users. Thanks for pointing this out.

    Post edited by bshifaw on
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