I am pretty new to the cancer field and now try to run MuSiC for WashU to detect significantly mutated genes in our exome-seq samples. Since I am not sure if I am doing the right things I would appreciate if someone can take a look at what tools I am using. Probable there is a lot room for improvements. So here are the steps I am running to get significantly mutated genes:
- FastQ files
- BWA map to reference genome
- Mark duplicates by picard tools
- Use GATK to InDel realign and base recalibration
- samtools mpileup for each normal and tumor sample
- Somatic variation calling. I use VarScan somatic for this.
- snpEff to annotate the mutations and their consequences
- Convert VCF file from previous step to MAF file and filter for consequences that very likely change the gene function (e.g. missense)
- Combine filtered MAF files from all samples
- Run MuSiC bmr calc-covg
- Run MuSiC bmr calc-bmr
- Run MuSiC smg
Especially step 8 and 9 seem to be tricky. I am not sure if I am missing some straight forward solution from calling mutations to MAF files.