Hello,

For a lot of work, it is helpful to know the cM position of your snps. Here is a script that takes the linkage map produced by Chris, your snp table in Hapmap format, and adds a column giving you a cM position for each site. It interpolates between known positions, so individual positions the accuracy of the position is overstated, but it’s good for plotting.

https://github.com/owensgl/reformat/blob/master/hmp2cmpositions.pl

usage:

perl hmp2cmpositions.pl /moonriseNFS/HA412/pseudomolecules/lg.ALL.bronze14.path.txt yoursnptable.hmp > yoursnptable.withcm.hmp