Dear all in BioStar,
I have benefit much from your kind helps and directions. Thanks a lot. Here, I still want to get much more from you.
I have my NGS population genomic data (haplotypic data) in VCF format. I just took advantage of the excellent functionalities of VCFtools (option, --hap-r2) to calculate LD of pairwise SNPs. But, it is somewhat slow, usually one week for one chromosome.
(1) Here I would like to hearing your opinion on selecting a right tools for such LD (pairwise r-square) calculation. Other tools or efficient ways (2) And also, your advice or experience on generating LD decay plot are appreciated.
Thanks a lot for your helps in advance.
My objective is 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.
Don't really have experience calculating LD neither ploting it but perhaps this link in R-bloggers can help you. The author poste some R code for estimating the decay of LD according to Hill and Weir,
Hopefully it's of help, Regards,