LDBlockShow

LDBlockShow: a fast and effective tool for Show Region Linkage disequilibrium heatmap Figure analysis based on variant call format files

1) Install

Download

Method1 For linux/Unix and macOS

        git clone https://github.com/BGI-shenzhen/LDBlockShow.git
        chmod 755 configure; ./configure;
        make;
        mv LDBlockShow  bin/;    #     [rm *.o]

Note: If fail to link,try to re-install the libraries zlib

Method2 For linux/Unix and macOS

        tar -zxvf  LDBlockShowXXX.tar.gz
        cd LDBlockShowXXX;
        cd src;
        make ; make clean                            # or [sh make.sh]
        ../bin/LDBlockShow

Note: If fail to link,try to re-install the libraries zlib

2) Introduction

Linkage disequilibrium (LD) Blocks [1] is the most important and most common analysis in the population resequencing[2]. Special in the self-pollinated crops, the LD Blocks for Special region (seletion region,gwas region) is show more detailed information to pick the Specified genes. Compared with the other two softwares, the results of LDBlocksShow are the same and use less computing resources (DataSet at 1000 sample with 1000 sites). For ordinary users, LDBlocksShow is more friendly and simple to use

Software	Mem (G)	Cpu Time (h)	Result
Haploview4.2.jar	95	36	HeatMap+Block
R:Ldheatmap 0.99	1	48	HeatMap
LDBlockShow 1.03	1	1	HeatMap+Block+GWAS

Parameter description

 ./bin/LDBlockShow

	Usage: LDBlockShow  -InVCF  <in.vcf.gz>  -OutPut <outPrefix>  -Region  chr1:10000:20000

		-InVCF        <str>     Input SNP VCF Format
		-OutPut       <str>     OutPut File of LD Blocks

		-Region       <str>     In One Region to show LD info svg Figture

		-BlockType    <int>     method to detect Block [beta]
		                        1: Gabriel Method 2 Solid Spine of LD [1]

		-help                   Show more Parameters and help [hewm2008 v1.03]

3) Example

See more detailed Usage in the Chinese Documentation and see the example and Manual.pdf for more detailed

Example 1) show Figure with Defaut LD Blocks

../../bin/LDBlockShow   -InVCF Test.vcf.gz   -OutPut  out   -Region  Ghir_D11:24100000:24200000

Example Result Show

Example 2) show Figure with Defaut LD Blocks + GWAS

#../../bin/ShowLDSVG	-InPreFix	../Example1/out	-OutPut	out.svg	-InGWAS	gwas.pvlue
../../bin/ShowLDSVG	-InPreFix	../Example1/out	-OutPut	out.svg	-InGWAS	gwas.pvlue -Cutline  7

Example Result Show

Example 3) show Figure with Plinks LD Blocks

./plink-1.9/plink	--vcf	../Example1/Test.vcf.gz	--geno	0.1	-maf 0.01 --blocks  no-pheno-req --out	plink	--allow-extra-chr
cp  ../Example1/out.* ./;  
rm  out.blocks.gz  ; mv    plink.blocks.det   out.blocks ; gzip  out.blocks ; rm  plink.*
../../bin/ShowLDSVG  -InPreFix   ./out   -OutPut out.svg

Example Result Show will be the same with Example 1)

Exampl 4) show Figure with Plinks LD Blocks + GWAS

#../../bin/ShowLDSVG	-InPreFix	../Example3/out	-OutPut	out.svg	-InGWAS	gwas.pvlue
../../bin/ShowLDSVG	-InPreFix	../Example3/out	-OutPut	out.svg	-InGWAS	gwas.pvlue -Cutline  7

Example Result Show will be the same with Example 2)

4) Results

A LD heatMap images which I draw before.

5) Discussing

📧 hewm2008@gmail.com / hewm2008@qq.com
join the QQ Group : 125293663

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milkcookie/LDBlockShow