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Indel realignment for a normal-tumor pair of BAM files

dgacquerdgacquer BelgiumPosts: 2Member

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



Best Answer


  • dgacquerdgacquer BelgiumPosts: 2Member

    Thanks Geraldine,

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

    Best regards


  • artitandonartitandon Posts: 22Member

    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 Posts: 10,569Administrator, Dev admin

    Yes it is.

    Geraldine Van der Auwera, PhD

  • artitandonartitandon Posts: 22Member


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