I have been trying to use LDHAT to estimate recombination rates however I am having some issues regarding likelihood tables.
So, I have a vcf file of 50 individuals which I converted to *.locs and *.sites format using vcftools. As there are 50 individuals (100 chromosomes), so I use the n=100 likelihood file as in: https://github.com/auton1/LDhat/blob/master/README.md
But when I use ./pairwise to estimate recombination rates it gives me this error:
Likelihood file for different no. seqs than data
Can anybody help me out as to why am I getting this error repeatedly?