Problems in running LDHAT

Question

[Shab86]

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

[timothy.delory]

Hello Sabeer,

I am encountering this exact problem myself. Were you able to resolve this?

[Shab86]

Hei Timothy,

I am not sure what I did back then, but I remember using 96 individuals, converting the phased vcf file to locs/sites using vcftools, renaming the .sites file to .seq file and then using likelihood file for n=192.

 ./interval -seq phased.ldhat.seq -loc phased.ldhat.locs -lk lk_n192_t0.001 -its 60000000 -bpen 5 -samp 40000

Hope this helps!