LDdecay计算和做图

先下载PopLDdecay软件（开源GitHub）

https://github.com/BGI-shenzhen/PopLDdecay

PopLDdecay的安装

1) INSTALL  Method1
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Just execute as follows :
	git clone https://github.com/BGI-shenzhen/PopLDdecay.git
	chmod 755 configure ; ./configure ;
	make;
	mv PopLDdecay  bin/ ;
**Note:** If fail to link,try to <b>re-install</b> the libraries [**_zlib_**](https://zlib.net/)
2) INSTALL Method2
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A) Method2 For linux/Unix
	For linux/Unix , execute as follows :
			 tar -zxvf  PopLDdecayXXX.tar.gz
			 cd PopLDdecayXXX;
			 cd src;
			 make ; make clean
			 ../bin/PopLDdecay
	#I had compiled and installed these gz library packages [zlib] on the linux X64 platform
	if Link do not work ,try Re-install the gz library and copy them to the library Dir
	        	 PopLDdecayXX/src/include/zlib 

B) Method2 For macOS  platform INSTALL
	you should  must  pre-install the library [zlib] and copy them to the corresponding library directory
	#step1 :Should must <b>re-install</b> the gz library [zlib]
			  see  [zlib] website
	#step2  :  # Copy these gz library file into the corresponding library directory
			  cp libz.a libz.so*  PopLDdecayXX/src/include/zlib
	#step3  :
	          sh make.sh # or [make && make clean]

C) Other Method
Note if it can't work . follow below  B1-B6  or use the  static Compiled [BamDeal_Linux ]
############################################
	   #autoscan ./
	   #cp configure.scan configure.ac
# if can't work,  follow below 6  commands
	  B1:     aclocal             #//   src/automake-1.9/aclocal
	  B2:     autoconf            #//   src/automake-1.9/autoconf
	  B3:     autoheader          #//   src/automake-1.9/autoheader
	  B4:     automake --add-missing   #//  src/automake-1.9/automake  --add-missing
	  B5:      ./configure
	  B6:      make
#############################################
#swimming in the sky & flying in the sea#

　　

PopLDdecay的使用

step1

查看PopLDdecay的使用方法

sample:

# 1)  For gatk VCF file deal , run PopLDdecay  direct
          ./bin/PopLDdecay    -InVCF  SNP.vcf.gz  -OutStat Lddecay.stat.gz
# 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.stat.gz
# 3)  To Calculate the subgroup GroupA LDdecay in VCF Files   # put GroupA sample names into GroupA_sample.list file
          ./bin/PopLDdecay   -InVCF    -OutStat    -SubPop    GroupA_sample.list

　　

step2:

sample: