shapeIt - prephasing - 1000g genetic map

Question

[muralinmars]

Hi all,

I am using shapeit to prephase the genotypes, followed by using minimac to do the imputations (with 1000g phase1 v3 as the reference panel)

Now when I phase the genotypes - I would like to use the genetic map from 1000g instead of the hapmap genetic map that is mentioned in shapeit manual..

Is it possible for someone to direct me to the right source.. also it would be great if you can correct if my reasoning is wrong.

Thanks

Answer 1

[trausch]

Have you checked the Impute2 1000 Genomes phase 3 reference data?

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

[Kevin Blighe]

I have accepted this answer on behalf of the OP