.map file for Impute2

Question

[lmh327]

How do I generate .map files that I need to use in Impute2 as input?

I have binary files (bed, bim, fam) that are from PLINK output. Using --recode I get a .ped and .map file but this map file does not work in Impute2 because it does not have the right number of columns. I am willing to use any program to get the .map file, but I'm not sure what my other options are.

Where do you get a .map file

Thanks!

Answer 1

[chrchang523]

Impute2 expects a recombination map file which you can obtain from https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference, not a PLINK .map file. (Yes, the identical file extension is confusing.)

[lmh327]

Follow up question: Does it matter that my variant that I am going to try to impute from my reference panel into the GWAS study is not part of the map file (it has not be looked at before).

Essentially I have taken the reference panel, genotyped my variant an added it to the SNP data already available for those individuals. This combined file was phased using SHAPE-it to with the output in the HAPS/SAMPLE format. I manually made the legend file since I am looking at a small region. I now downloaded the map file as you indicated. When I run IMPUTE2 I get a segfault (core dump) error. If I look at it as carefully as I understand, it appears that all of the files were loaded properly but if I look at the "data processing" section it says that all SNPs are present in both files (the reference panel and GWAS) and this should not be the case.

Do you have any thoughts on this or the more specific question: Does it matter that my variant is not in the .map file?

If it does, how do I add it to the map file?

Thank you for your answer! The identical file extensions is really confusing for a novice computational scientist.