I often need to know the interpolated cumulative genetic distance in cM across the genome. I am aware of some software, such as shapeit4, which outputs an INFO field in the vcf:
##INFO=<ID=CM,Number=A,Type=Float,Description="Interpolated cM position"> 9 204201 rs10964134 G A . . AC=0;AF=0.170557;CM=0;AN=2 GT 0|0 9 204485 rs613181 T C . . AC=1;AF=0.227743;CM=0.000228;AN=2 GT 0|1 9 206132 rs10757083 A C . . AC=0;AF=0.218573;CM=0.002086;AN=2 GT 0|0 9 212486 rs118002206 G A . . AC=0;AF=0.0163388;CM=0.00778367;AN=2 GT 0|0
It's possible to manually calculate and then use bcftools annotate to add it in, but this is a bit of a hassle.
Does anyone know of any software which I can give a) my vcf, and b) a genetic map, which will then annotate the vcf with an INFO field which gives the interpolated cumulative genetic distance?