Re: [Ldhat-help] lookup table

[Adam A. <ada...@gm...>]

It is too computationally intensive to generate a lookup table at that scale. You should consider thinning your data to 192 chromosomes, as the results are unlikely to change much for larger samples. 

Adam
Sent from my iPhone

> On Oct 8, 2015, at 16:15, Yogendra Khedikar <ykh...@gm...> wrote:
> 
> Hi,
> I have 631 individuals and would like to generate lookup table for recombination estimation.
> Could you please suggest me how can I generate new lookup table for 631 individuals.
> I tried rhomap using existing lookup table, but it doesn't work.
>  
> ./rhomap -seq chr1.ldhat.sites -loc chr1.ldhat.locs -lk lk_n192_t0.001
>  
> Starting rate estimation
> Seed = -1444335004
> 
> How many updates for MCMC? 1000
> 
> Number of updates between samples:10
> 
> Input number of Burn In iterations:1000
> 
> Analysing 631 genotypes of length 776 seg sites
> Reading sequences in fasta format
> Run-time error...
> Likelihood file for different no. seqs than data
> ...now exiting to system...
> Bye!
> 
> Thanks in advance!
>  
> Regards,
> Yogendra
>