Analysis in the recent Cell paper by Hodis et al

Katja

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?

Geraldine_VdAuwera

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.

Katja

Thank you Geraldine.