We looked more into this, and found that although this mutation is not present in our WGS bam file, it is present in Sanger’s WES bam file (there are 4 reads out of 39 that are mutated). This is a COSMIC and TCGA hotspot (and has been reported in dbSNP). Our pipelines tend to rescue hotspot mutations even if they originally get filtered in mutation calling. It is possible that we have rescued this mutation in our pipelines even though it has low allele frequency, whereas Sanger has not. If so this may be a case where DepMap and Sanger lines have diverged, or we do not have sufficient read depth to detect a rare cell line subclone.