PopLDdecay
The PopLDdecay article has been published in Bioinformatics magazine, please cited this article if possible
PMID: 30321304 Â Â Â Â Â Â Â Â Â DOI:10.1093/bioinformatics/bty875
1) Install
The new version will be updated and maintained in hewm2008/PopLDdecay, please click below website to download the latest version
Method1 For linux/Unix and macOS
git clone https://github.com/hewm2008/PopLDdecay.git
cd PopLDdecay; chmod 755 configure; ./configure;
make;
mv PopLDdecay bin/; # [rm *.o]
Note: If fail to link,try to re-install the libraries zlib
Method2 For linux/Unix and macOS
tar -zxvf PopLDdecayXXX.tar.gz
cd PopLDdecayXXX;
cd src;
make ; make clean # or [sh make.sh]
../bin/PopLDdecay
Note: If fail to link,try to re-install the libraries zlib
2) Example
see more detailed Usage in the Documentation
-
- Calculate LD decay
# 1) For gatk VCF file deal , run PopLDdecay direct
./bin/PopLDdecay -InVCF SNP.vcf.gz -OutStat LDdecay
# 2) For plink [.ped .map], chang plink 2 genotype first 2) run PopLDdecay
perl bin/mis/plink2genotype.pl -inPED in.ped -inMAP in.map -outGenotype out.genotype ; ./bin/PopLDdecay -InGenotype out.genotype -OutStat LDdecay
# 3) To Calculate the subgroup GroupA LDdecay in VCF Files # put GroupA sample name into GroupA_sample.list
./bin/PopLDdecay -InVCF -OutStat -SubPop GroupA_sample.list
-
- 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
- Parameter description
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 v3.42]4) Results
some LD decay images which I draw in the paper before.
5) Discussing
📧 [email protected] / [email protected]- join the QQ Group : 125293663
- PopLDdecay article has been published in Bioinformatics magazine, please cited this article if possible
- PMID: 30321304 Â Â Â Â Â Â Â Â Â DOI:10.1093/bioinformatics/bty875
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