Hi all,

I'm trying to build a custom reference panel for use with IMPUTE2. I have a phased .vcf from all my participants, and I was using [the first script here][1], modified slightly to work with my vcf/HG38, to build the reference panel. The exact command I run to generate the files for chromosome 1 (as an example) is:

    ./vcf2impute_legend_haps.pl -vcf my_vcf.vcf.gz \
      -leghap output_prefix \
      -chr chr1  \ 
      -hg38

The -hg38 thing is just an argument I added to the script, and can be ignored.

This generates .hap.gz files, .legend.gz files, and .sample_list files, one for each chromosome. What I'm missing is a genetic map file. I don't what these are, and I can't find anything on it in the documentation. Looking at the 1000 Genomes HG37 reference panel files provided [here][2], it's not clear to me what these mapping files are, so I can't replicate the steps to create them.

Any advice would be appreciated. 


  [1]: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#scripts
  [2]: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference
According to the documentation you linked, genetic maps are recombination maps, measured in centiMorgans. 

If you can lift-over the genomic position of the markers from the 1000 Genomes HG37 reference panel, you can use the same genetic map position (the **Genetic_Map(cM)** column), and recalculate the recombination rate between current position and next position in map (the **COMBINED_rate(cM/Mb)** column).

However, are you sure there isn't an updated version of these files?