PopLDdecay
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
Install / Use
/learn @BGI-shenzhen/PopLDdecayREADME
PopLDdecay
The <i><b>PopLDdecay article</b></i> has been published in <b> Bioinformatics magazine</b>, please cited this article if possible
PMID: 30321304 DOI:10.1093/bioinformatics/bty875
1) Install
The <b>new version</b> will be updated and maintained in <b>hewm2008/PopLDdecay</b>, please click below website to download the latest version </br><p align="center"><b>hewm2008/PopLDdecay</b></p>
<b> Download </b>
</br> Method1 For <b>linux/Unix</b> and <b> macOS </b> <pre> git clone https://github.com/hewm2008/PopLDdecay.git cd PopLDdecay; chmod 755 configure; ./configure; make; mv PopLDdecay bin/; # [rm *.o] </pre>Note: If fail to link,try to <b>re-install</b> the libraries zlib
Method2 For <b>linux/Unix</b> and <b> macOS </b>
<pre> tar -zxvf PopLDdecayXXX.tar.gz cd PopLDdecayXXX; cd src; make ; make clean # or [sh make.sh] ../bin/PopLDdecay </pre>Note: If fail to link,try to <b>re-install</b> the libraries zlib
2) Example
see more detailed Usage in the <b>Documentation</b>
-
- Calculate LD decay
-
- draw the Figure
# 2.1 For one Population
perl bin/Plot_OnePop.pl -inFile LDdecay.stat.gz -output Fig
# 2.2 For one Population muti chr # List Format [chrResultPathWay]
perl bin/Plot_OnePop.pl -inList Chr.ResultPath.List -output Fig
# 2.3 For muti Population # List Format :[Pop.ResultPath PopID ]
perl bin/Plot_MutiPop.pl -inList Pop.ResultPath.list -output Fig
-
- see the result [LDdecay.stat.gz] and [Fig.png Fig.pdf]
3) Introduction
Linkage disequilibrium (LD) decay[1] is the most important and most common analysis in the population resequencing[2]. Special in the self-pollinated crops, the LD decay may not only reveal much about domestication and breed history[3], but also can reveal gene flow phenomenon, selection regions[1].However, to measure the LD decay, it takes too much resources and time by using currently existent software and tools. The LD decay studies also generate extraordinarily large amounts of data to temporary storage when you using the mainstream software "Haploview"[4], the classical LD processing tools. Effective use and analysis to get the LD decay result remains a difficult task for individual researchers. Here, we introduce PopLDdecay, a simple- efficient software for LD decay analysis, which processes the Variant Call Format (VCF)[5] file to produce the LD decay statistics results and plot the LD decay graphs. PopLDdecay is designed to use compressed data files as input or output to save storage space and it facilitates faster and more computationally efficient than the currently existent softwares. This software makes the LD decay pipeline significantly
- <b> Parameter description</b>
Usage: PopLDdecay -InVCF <in.vcf.gz> -OutStat <out.stat>
-InVCF <str> Input SNP VCF Format
-InGenotype <str> Input SNP Genotype Format
-OutStat <str> OutPut Stat Dist ~ r^2 File
-SubPop <str> SubGroup SampleList of VCFFile [ALLsample]
-MaxDist <int> Max Distance (kb) between two SNP [300]
-MAF <float> Min minor allele frequency filter [0.005]
-Het <float> Max ratio of het allele filter [0.88]
-Miss <float> Max ratio of miss allele filter [0.25]
-EHH <str> To Run EHH Region decay set StartSite [NA]
-OutFilterSNP OutPut the final SNP to calculate
-OutType <int> 1: R^2 result 2: R^2 & D' result 3:PairWise LD Out[1]
See the Help for more OutType [1-8] details
-help Show more help [hewm2008 v3.43]
4) Results
some LD decay images which I draw in the paper before.
5) Discussing
- :email: hewm2008@gmail.com / hewm2008@qq.com
- join the<b><i> QQ Group : 125293663</b></i>
- <i><b>PopLDdecay article</b></i> has been published in <b> Bioinformatics magazine</b>, please cited this article if possible
- PMID: 30321304 DOI:10.1093/bioinformatics/bty875
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