Analysis in the recent Cell paper by Hodis et al

KatjaKatja Posts: 2Member
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 Posts: 8,027Administrator, GATK Dev 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

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,027Administrator, GATK Dev 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

  • KatjaKatja Posts: 2Member

    Thank you Geraldine.

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