I am trying to impletement
rehh2 to identify signatures of selection with
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
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?