where can i find the GRCh38 genetic map for IMPUTE2

Question

[raalsuwaidi]

Hi all,

any advice on where i can find the genetic map for the GRCh38 version of 1000Genomes? this is needed as a parameter in the imputation process by IMPUTE2.

[4galaxy77]

impute2 is extremely outdated now, its nearly 10 years and and 3 versions have been released since then. Unless there is a very good reason, you should be using impute5 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009049

[raalsuwaidi]

thanks for the recommendation. the reason behind using IMPUTE2 is the -merge_ref_panels option which is not available in IMPUTE5

[4galaxy77]

why not just merge them using e.g. bcftools before and then run IMPUTE5?

[raalsuwaidi]

the idea behind the -merge_ref_panels from IMPUTE5 is that it merges one reference panel into the other then use the output for imputation. i am interested to see is one reference panel would be unable to impute the rare variants and hence the impact on the imputation process

[zx8754]

• IMPUTE2- Map file for custom reference panel
• 1000 genomes project reference panel - GRCh38
• Where to get genetic map build 38 ?

Answer 1

[raalsuwaidi]

hi all,

i finally found the genetic map for build GRCh38. it is at the below link if anyone needs to have it

https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/