Issue with map file output from plink

Question

I am working with the vcf file (generated using bcftools) to create a map file using plink software. The command i am using is

./plink --vcf sample.vcf --out sample --recode --allow-extra-chr 

The output .map file looks like this

CM004562.1  .   0   1645
CM004562.1  .   0   4771
CM004562.1  .   0   4811
CM004562.1  .   0   4812
CM004562.1  .   0   5001
CM004562.1  .   0   5672
CM004562.1  .   0   5674
CM004562.1  .   0   5678
CM004562.1  .   0   5684
CM004562.1  .   0   5802

Why it outputs zero in the 3rd column?, and how to fix that?

Answer 1

The third column of the map file represents the position of the variants based on the recombination map: https://www.cog-genomics.org/plink/1.9/formats#map

This field is optional and I assume your input VCF file doesn't have the info.

You can get the recombination map from other resources, such as 1000 Genomes: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

Once you have the recombination map of your choice, you can use Python/R to replace the third column with the position in centimorgans.