How to started on SNP analysis

Question

[cyril-cros]

Hi guys,

I have so far acquired some experience on RNASeq (annotation, differential expression etc...), and I majored in bioinformatics. I am starting a PhD, and would like to spend a short rotation in a lab doing human genetics: analysis of SNPs and recombination under an evolutionnary angle (comparing different groups and/or chimps).

Do you have any good tutorial for that kind of research? Or article references, with a good methods and materials section?

Thanks

Answer 1

[h.mon]

Two of the most commonly used provide detailed guides:

1. GATK best practices
2. SAMtools mpileup