Annotating a .vcf with centimorgan information Some programs (e.g. shapeit4) automatically annotate an INFO tag into a .vcf file which gives the cumulative genetic distance in cM between each SNP:
##fileformat=VCFv4.2
##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
##fileDate=10/11/2020 - 21:29:39
##source=G2H
##contig=&lt;ID=9&gt;
##INFO=&lt;ID=AF,Number=A,Type=Float,Description=&quot;Allele Frequency&quot;&gt;
##INFO=&lt;ID=AC,Number=1,Type=Integer,Description=&quot;Allele count&quot;&gt;
##INFO=&lt;ID=CM,Number=A,Type=Float,Description=&quot;Interpolated cM position&quot;&gt;
##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;Phased genotypes&quot;&gt;
##INFO=&lt;ID=AN,Number=1,Type=Integer,Description=&quot;Total number of alleles in called genotypes&quot;&gt;
##bcftools_viewVersion=1.9-207-g2299ab6+htslib-1.9-271-g6738132
##bcftools_viewCommand=view -s -1_-1 ukb_cal_chr9_v2.HumanOrigins.common_snps.HumanOriginsInds.fiftyPercentEthnicUKBInds.PHASED.bgz.vcf.gz; Date=Mon May 24 14:15:51 2021
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  -1_-1
9   257034  rs573860    A   G   .   .   AC=0;AF=0.388699;CM=0;AN=2  GT  0|0
9   270321  rs17720310  A   G   .   .   AC=0;AF=0.0820595;CM=0.007994;AN=2  GT  0|0

However, this program is really used for phasing not for .vcf annotation.
Ideally I'd like a simple command line program which takes input the .vcf and a genetic map and interpolates the genetic distance and adds a cumulative map. This could be done manually with a custom script, but quite frankly I can't be bothered to do that.
Does anyone know of a tool that exists which will do this?
I posted this to biostars a while ago and received one reply which linked to this post, which includes links to tables containing cM locations for different rs numbers.
EDIT: I am interested in doing this for human data (although the same would be the case for any diploid organism).
I think a useful tool to address your question is QCTOOL v2. Particularly, the option you are looking for is -annotate-genetic-map. This tool has been developed originally for GWAS datasets. It has multiple inputs data format.
If you could provide input data as an example, I will try working on it to provide the necessary steps to be done.
Hope this answers your question.