Analysis in the recent Cell paper by Hodis et al
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?