Scanning for selection using rehh2 from mouse WGS VCF
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2.6 years ago
serpalma.v ▴ 70

Hello

I am trying to impletement rehh2 to identify signatures of selection with iHS.

I have a vcf file, fresh out of the gatk pipeline and I see it needs to be phased. I intend to do this with shapeit2 which requires a genetic map.

Once the phased haplotypes are ready, I should be able to run the R package reeh2, which needs the ancestral alleles.

My questions are the following:

(1) Where can I get the official genetic map for mouse?

(2) Where can I get a file with the ancestral and derived allele information for mouse?

Thanks!

rehh2 sequencing mouse • 596 views