Hi everyone,

I am currently conducting a selection scan (XPEHH) using selscan v2.0. I have phased VCF files (phased using Eagle) and I need to prepare the corresponding .map files that include genetic distances (cM).

My plan is to use PLINK to interpolate the genetic map positions from a reference map into my VCF data. I am using the GRCh37 genetic map provided by BEAGLE (specifically plink.chr*.GRCh37.map from https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/).

Here is the command I am using:

plink --vcf my_phased_data.vcf.gz \
  --chr 5 \
  --cm-map plink.chr5.GRCh37.map 5 \
  --recode \
  --out test_chr5_correct

Is this the standard/correct way to generate the .map file required by selscan?

Does selscan directly accept the standard PLINK .map output format (Chrom, ID, cM, bp), or does it require any additional reformatting?