SNV Calling on Deep Sequencing Data (no normals)

[fongchun]

Hi,

Apologies if this question has been asked before, but I was wondering if anyone knows of a good protocol/tools to use for calling SNVs from targeted re-sequencing data (<100X) from cancer data without matching normal?

I've been using the GATK UnifiedGenotyper to do it so far, but I am not sure if this is the best protocol since from my understanding it wasn't designed with targeted re-sequencing in mind. I know there is deepSNV, but that appears to need both a normal and a tumour.

Any advice would be much appreciated!

Thanks,