MutSig creation of coverage table

Question

[ksymeonidh]

Deal all,

I have a cohort of 85 samples (unfortunately tumor only) and a second with 11 samples (tumor-normal). I was successful in a test run of MutSig, using the coverage file "exome_full192.coverage.txt", but I was wondering how to create the coverage table for the specific experiment. For the creation of the sequenced bases as well as the effect, I believe a combination of the bam and maf files is possible, but how to create the category column? My exome data were generated using the SureSelect V4 kit for the 85 samples and V3 for the 11 tumor-control samples. The maf files are created using the VEP program, hen converting the vcf file to mar with vcf2maf and concatenating the samples together.
Any ideas would be really appreciated.

Thank you in advance

Answer 1

[achristofferson]

Mixing the two capture kits makes for fun times. I would make a coverage file that is specific to the V4, sense it represents the majority of your data. CovGen can make a capture/target specific coverage table for you.