Question: Problems in running LDHAT
0
gravatar for Shab86
7 months ago by
Shab86220
Helsinki
Shab86220 wrote:

Hi all,

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?

Thanks, Sabeer

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