Exome-seq: looking for common mutations among my samples

[blakeoft]

Hello,

I've got vcf files for several samples with the same type of cancer. Is there a way to find the genes that are most commonly mutated among my samples? I'm assuming that a series of unix piping commands paired with a list of genes and coordinates will do the trick. Is there perhaps some software that already does this?

Thanks,
Blake

[Brian Bushnell]

This is actually incredibly difficult. Entire deleted genes or exons will probably not show up at all in the VCF file, and mutations in introns, promoters, and other non-exonic locations are hard to annotate. If you limit your study to, say, nonsense and frameshift mutations, then it's doable (though I can't give you any suggestions on software), but it's not clear how useful that will be.