The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Analysis in the recent Cell paper by Hodis et al

KatjaKatja Member Posts: 13
edited July 2012 in Ask the GATK team

Dear developers,

in the recent Cell paper by Hodis et al (Broad Institute) using GATK for somatic mutation calling, authors report filtering indels that were "supported by reads with a high average number of additional mismatches and calls made in genomic loci covered by reads with a high average mismatch rate and low base quality". It is pointed out in the paper that this is a part of GATK. I haven't been able to locate the corresponding algorithm. Could you please point me to the walker/function?

Post edited by Carneiro on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,015 admin
    Answer ✓

    The main tool to do this is the SomaticIndelDetector. Note that, as far as we know, the cancer group does do some extra processing (which should be discussed in the paper) so if you need full details I would recommend asking the authors directly.

    Geraldine Van der Auwera, PhD


Sign In or Register to comment.