Calculation of LD decay value in GWAS

Question

[divya.sharma19899]

I have performed GWAS of morphological data with SNPs generated through genotyping by sequencing(GBS) approach through TASSEL software but i dont have the reference genome. i want to calculate LD decay values and assign qtls on the map based on ld decay values. Please tell me how to calculate LD decay values. kindly help out.

[Kevin Blighe]

I kindly ask that you take a look at rmf's great answer, here: LD-decay in a r2 vs distance(cm) plot

Answer 1

[hewm2008]

Here, I introduce PopLDdecay, a simple- efficient software for LD decay analysis, which processes the Variant Call Format VCF5 file to produce the LD decay statistics results and plot the LD decay graphs.

The simple used :

 
./bin/PopLDdecay    -InVCF  SNP.vcf.gz  -OutStat LDdecay  
perl  bin/Plot_OnePop.pl  -inFile   LDdecay.stat.gz  -output  Fig

[HZZ0036]

Hi, I used PopLDdecay, but the output figure is not a curve.

[hewm2008]

maybe your snpdata is too samlll , you can use the modify the para [ -bin1 -bin2 ] to get the curve