Advice on my study and parameters for complete

[ptranvan]

Hi,

I am working on a non model organism and I am looking to estimate recombination rate along my genome and different part of the genome (ex chromosome, within chromosome etc.)

I have RADseq data of a family: parents and multiple offsprings and did a simple snp calling using Stacks in order to obtain a vcf file.

Now I a bit struggled about the following step.

1. are the parents needed or I can compute the recombination rate just with the offpsrings ?

2. I sorted my vcf with vcf-sort and convert with vcftools to ldhat .sites and .locs using vcftools then I did a quick test for one chromosome:

convert -seq chr1.ldhat.sites -loc chr1.ldhat.locs

I got a result but I am not sure how ton interpret it:

Summary of output data

Segregating sites      =      786
Average PWD            =  339.222
Watterson theta        =  138.827
Tajima D statistic     =    4.717
Fu and Li D* statistic =    3.062

3. I want to create a lookup table with complete: it asked me the theta, is it the one estimated above ? Watterson theta.

Am I doing right ?

Thanks

[viannam]

Hi @ptranvan,

Try to select a subset of your data and run the pairwise, or other programs of LDhat, that gives you the suggested theta per site. Will be 0.01 or 0.001 depending on your study, as you can see in the ik files examples.