How to generate MAP file?

Question

[sjunlee89]

I have .bim, .bgen, pgen, .fam files for analysis GWAS.

I would like to generate .map file to use Haploview software to make LD heatmap.

On the other hand, I have no idea how to make map file from .bim, .bgen, .pgen, .fam files.

Could you explain the process by plink or plink2.

Thank you advanced.

Answer 1

[Kevin Blighe]

You can read your data into PLINK with the --bgen flag. After, you can output the data in Haploview format with, for example:

plink --noweb --bfile MyData --chr 5 --from-bp 135364584 --to-bp 135399507 --snps-only no-DI --recodeHV --out MyData.HV ;

I then have this line written in my notes, which is likely still valid:

Start Haploview. In the ‘Welcome to Haploview’ window, select the ‘LINKAGE Format’ tab. Click the ‘browse’ button to enter the ‘Data File’ and select the PED file ‘MyData.ped’. Click the ‘browse’ button to enter the ‘Locus Information File’ and select the file ‘MyData.hmap’.

Kevin

[sjunlee89]

Thank you so much for your comment.