Error: target chromosome not found in genetic map file

[WeiYang-BAI]

Hi, I am running minimac v4.1.6 but keep getting an error with the --map flag. However, the imputation process seems okay:

"Error: target chromosome not found in genetic map file."

My genetic map for hg38 looks like this: chr position COMBINED_rate(cM/Mb) Genetic_Map(cM) 1 785910 2.6858076690 0.410292036939447 1 788439 2.8222713027 0.417429561063975 1 788511 2.9813105581 0.417644215424158

I also tried this, but the error persists: chr position COMBINED_rate(cM/Mb) Genetic_Map(cM) chr1 785910 2.6858076690 0.410292036939447 chr1 788439 2.8222713027 0.417429561063975 chr1 788511 2.9813105581 0.417644215424158

Any ideas? Or is there a recommended genetic map for GRCh38 when using minimac4?

Best regards,

[jonathonl]

The recommended format is below (# needed on first line and tabs instead of spaces).

#chr\tposition\tGenetic_Map(cM)
chr1\t785910\t0.410292036939447
...

This should have exited after the error instead of continuing to run imputation. That needs to be fixed.

[jonathonl]

Try https://share.sph.umich.edu/minimac4/map_files/genetic_map_hg38_withX_3cols.tsv.gz.

[WeiYang-BAI]

Thanks, @jonathonl !