julianhess

BTW, it looks like we have to update the test suite VM to include an installation of htslib.

I've confirmed this works with Strelka VCFs, both malformed and header fixed. Need to test on M2 and Sanger before merging.

Hi Rupal, Running MutSig on a cohort with a large mutation overlap between samples will yield very poor results. MutSig's background model explicitly assumes that mutations arise independently across samples,...

Hi @walaj, If it's any help, I've made these fixes in my forked branch: https://github.com/julianhess/SeqLib/commits/jhess Apologies for not PR'ing this years(!) ago. —Julian

Hi @yusufdjuanda, Please see the following instructions for hg38 usage: https://github.com/getzlab/MutSig2CV/issues/10#issuecomment-1142375852

Yes, it is likely due to the size of your cohort. The "minimum cohort size" depends completely on the population frequency of drivers you want to discover, which is a...

Generally, the duplicate patient filter only gets activated when samples share many mutations because they are not from completely independent tumors, which violates MutSig’s statistical model. Are some of the...

>No, all my 13 samples are completely independent from one another. In that case, it sounds like something is wrong with your mutation calls. Here is the criterion used for...

Hi, The mutation type dictionary is the same between hg19 and hg38. Please use the file from the hg19 bundle. —Julian

Some of the files have been renamed between hg19 and hg38. Following the instructions in [this post](https://github.com/getzlab/MutSig2CV/issues/10#issuecomment-1142375852) should give you everything you need.