Question: Problems in running LDHAT
0
gravatar for Shab86
3.2 years ago by
Shab86250
Helsinki
Shab86250 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

genome • 1.1k views
ADD COMMENTlink written 3.2 years ago by Shab86250
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1185 users visited in the last hour