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Calculation of LD decay value in GWAS

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.

snp next-gen
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updated by hewm2008 • hewm2008 • written by divya.sharma19899 • divya.sharma19899

1 answer

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
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written by hewm2008 • hewm2008

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

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written by HZZ0036 • HZZ0036

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

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written by hewm2008 • hewm2008

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