Hi all,
sample TCGA-13-0889 in this dataset appears to have 1100 insertions and 6 SNPs. I found this very strange - probably a technical issue? I'm not sure if there are other samples like that.
Thanks,
Atanas
Created by nasko88 Thank you very much for looking into this! We've taken a closer look at that sample, and while it is weird, we don't think its caused by the computational pipeline (ie some sort of error in copying files around). The controlled access file MC3 file has ~180 mutations, but most of those are filtered out once we've applied the filters to ensure only somatic mutations are listed.
Also, this is a WGA (Whole Genome Amplification) sample, which has been known to introduce indel artifacts.