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Realignment (reference liftover) workflow or service in FireCloud

ncamardancamarda DFCIMember, Broadie


I was wondering if a workflow / service exists on FireCloud for realigning BAMs (aligned to a non-standard reference) to the Broad’s hg19 reference. I recognize that a WDL exists for realignment to hg38, but rather than fixing this workflow to do what I need, I was hoping a workflow / service already exists. Please let me know, and thank you for your consideration!



  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    I'm afraid that I'm not familiar with a WDL like that, but I can certainly look for you. Do you know the name of the workspace/method that realigns to hg38? There's often a paired one for hg19, if we are the original publishers of the method.

  • ncamardancamarda DFCIMember, Broadie

    Hi Kate - the link to the WDL for hg38 is here https://portal.firecloud.org/#workspaces/help-gatk/five-dollar-genome-analysis-pipeline

    Thank you so much for your help! I sincerely appreciate your time and energy.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    I think I may be misunderstanding you here. The workspace you linked takes in unmapped bams and aligns them--it doesn't handle already aligned bams and realign them. If you have already aligned bams, that workflow won't work for you either.

    If you have unmapped bams, though, you can use this workspace, which will align your bam to the b37 reference genome (aka hg19).

    I'm also going to speak with the author of the $5 Genome Analysis pipeline that you linked above and see if it would be possible to simply swap the reference file in the config for b37. There may be more that goes into it, so I want to be sure before recommending that route.

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