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ways to speed up Indel Realinger

Dear GATK-Team,

I am trying to speed up the Indel Realigner step in my pipeline. I have tried Queue, using number of scatters (-nsc) equal to 8; I noticed the jobs that are "scattered" finish relatively quickly (within 2 hours), but the Gather step is taking the bulk of the processing time (over 6 hours). I suspect this slow-down is because the scheduler for the cluster automatically assigns the Gather job to be done on just one core.

As I don't know enough about Queue and .scala to increase the number of cores for the Gather job, I was thinking of other ways to get the same output, but save time. Reading this post by @neilw in the forum (http://gatkforums.broadinstitute.org/discussion/3051/parallelizing-printreads), I was wondering if this approach would work:

1) Use RealignmentTargetCreator to get list of target intervals for realignment
2) Run 100 parallel jobs of IndelRealigner, passing to each the same (whole) input .bam and list of target intervals from step 1, but a unique portion of the genome using the -L option (intervals)
3) Merge the 100 realigned .bams with samtools to get single re-aligned .bam

Thanks a lot for your advice,

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Steve,

    That looks fine, but you can run RealignerTargetCreator on the unique intervals instead of starting using the intervals at the IndelRealigner step.


  • newGATKusernewGATKuser CaseMember

    Hi Sheila,

    Thank you for the reply! Sorry, I just realized I wasn't very clear in my original post. The intervals I would use in step 2 with the -L option are actually 100 equal parts spanning the whole genome (so IndelRealigner would create a re-aligned .bam for 1/100th of the genome). In that case, I probably won't get a speed-up passing these intervals to RealignerTargetCreator?


  • newGATKusernewGATKuser CaseMember

    Hi Sheila,

    Thank you for the good point! I had not thought of how Indel Realigner would treat reads that span intervals. I will try splitting by contigs to avoid this problem.


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