how to generate genetic maps from VCF snps data

Question

[mab658]

Hi Everyone,

Could someone guide me on how to generate genetic map from snps VCF file in order to use it for imputation. I have filtered my snps VCF file and I need genetic map for the imputation. I got to know that one can use PLINK. I need to know what I need to extract from my data prior to using PLINK. Thanks

Answer 1

[Kevin Blighe]

The genetic maps are available from here:

• https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

I also have them saved on my own online storage.

Kevin