GATK licensing moves to direct-through-Broad model -- read about it on the GATK blog

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

David

Tagged:

Best Answer

Answers

  • dgacquerdgacquer BelgiumPosts: 2Member

    Thanks Geraldine,

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

    Best regards

    David

Sign In or Register to comment.