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.

Indel realignment for a normal-tumor pair of BAM files

dgacquerdgacquer BelgiumMember

Dear GATK team,

I have noticed that sometimes, when I run IndelRealigner independently on a tumor BAM file and its matching normal BAM file, I get different haplotypes, leading to false somatic variant or indel calls. Is there a way to ensure that both BAM files are realigned the same way ? For instance, merging both BAM files together, running IndelRealigner and splitting resulting BAM file by read group ?

Best regards

David

Tagged:

Best Answer

Answers

  • dgacquerdgacquer BelgiumMember

    Thanks Geraldine,

    I did not known about the -nWayOut argument, this is exactly what I was looking for.

    Best regards

    David

  • artitandonartitandon Member ✭✭

    Is this the standard way to run Indel realignment for the tumor/normal samples, i,e. run it for both the normal and tumor sample together, and then use the -nWayOut option?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
  • IrantzuIrantzu Member
    edited December 2016

    Hi there!
    Maybe this has been asked before but if I have paired normal/tumor datasets, should I run both RealignerTargetCreator and IndelRealigner commands using both bam (N/T) files at time (for the both steps)?
    Thank you in advance,

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @Irantzu,

    If you are using a mutation caller that reassembles haplotypes, e.g. MuTect2, then there is no longer a need to perform indel realignment. If you are using a pile-up caller, e.g. MuTect1, then yes, please run RealignerTargetCreator and IndelRealigner on both your matched T/N BAMs concurrently. You can pass in multiple alignment BAMs each with the -I parameter. Generate one output file for each input by specifying -nWayOut instead of -o for IndelRealigner. For detailed documentation, see Tutorial#7156.

Sign In or Register to comment.