[Vcftools-help] how to do LD calculation by VCFtools

[Mao J. <jia...@gm...>]

Dear VCFtools-helpers,

I have benefit much from your kind helps and directions. Thanks a lot.

Here, I still want to get much more from you. This problem is not from any
errors/bugs of VCFtools. I just want to take advantage of the excellent
functionalities of VCFtools. I want to learn how to use the more complex
(for me) part of it.

I want to estimate the decay of LD, by resampling a starting point 10,000
times on a chromosome (here chromosome 1) for all the individuals in a VCF
file (mydata.vcf.gz). My data are haplotypic data (phased). The pariwise
haplotypic r2 need to be calculated for every pair of SNPs within 25-kb of
this starting point.

I read the online guide for:

   - --hap-r2
   - --geno-r2
   - --ld-window <int>
   - --ld-window-bp <int>
   - --min-r2 <float>

But, I am not clear how to do my this job. Could you please give my any
directions on this problem? Thanks in advance.

Best,
Jian-Feng, Mao


##########################################################
Here possible lines of command, please correct me.

# for this command, I do not know how to resampling a starting point 10,000
times on a chromosome
vcftools --vcf mydata.vcf.gz --chr 1 --hap-r2 ld-window 25000 --out
mydata.ld