Fastq Analysis For Loh Calls

Question

[Rima]

I have Illumina sequencing files i.e fastq files. These are intended to generate Loss of heterozygosity (LOH) calls on analysis. Could you suggest a analysis pipeline/s which could be used for the purpose?

Answer 1

[brentp]

A google search shows that VarScan does this but you'll have to align your reads first using a short-read aligner.

Also see this previous biostar question