Calculation of LD decay value in GWAS
1
0
Entering edit mode
3.7 years ago

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 • 3.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
3.7 years ago
hewm2008 ▴ 40

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
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1457 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6