使用PopLDdecay进行连锁不平衡分析

 

001、 软件下载：

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

 

002、下载最新版本

wget -c https://github.com/BGI-shenzhen/PopLDdecay/archive/refs/tags/v3.43.tar.gz

 

 003、解压、编译安装

tar -xzvf PopLDdecay-3.43.tar.gz
cd PopLDdecay-3.43/
chmod +x configure
./configure
make
mv PopLDdecay bin/
cd test/
./PopLDdecay

.

 

004、准备测试文件

[b20223040323@admin2 test5]$ ls
outcome.vcf

 

005、单群体运算

PopLDdecay -InVCF ./outcome.vcf -MaxDist 1000 -OutType 3 -OutStat out

 。

 

006、可视化

[b20223040323@admin2 test5]$ ls
outcome.vcf  out.LD.gz  out.stat.gz  snp.bin  snp.r
[b20223040323@admin2 test5]$ Plot_OnePop.pl -inFile out.stat.gz -bin1 10 -bin2 100 -break 100 -output snp
null device
          1
null device
          1

 。

 

007、

 

008、多群体的计算

[b20223040323@admin2 test5]$ ls
dor.list  gmm.list  outcome.vcf  sun.list
[b20223040323@admin2 test5]$ head -n 3 dor.list
DOR1
DOR2
DOR3
[b20223040323@admin2 test5]$ PopLDdecay -InVCF outcome.vcf -OutStat dor.stat.gz -SubPop dor.list
the Number of subPop samples[found in VCF] is 10
Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :7403
##begin pair-wise R^2 cal. after filter Remain SNP Number :     39246
#% number bin is        393
1%......-->100%.......          ALL done
Used [perl  ../bin/Plot_XX.pl ] to Plot the LDdecay
[b20223040323@admin2 test5]$ PopLDdecay -InVCF outcome.vcf -OutStat gmm.stat.gz -SubPop gmm.list
the Number of subPop samples[found in VCF] is 10
Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :5552
##begin pair-wise R^2 cal. after filter Remain SNP Number :     41071
#% number bin is        411
1%......-->100%.......          ALL done
Used [perl  ../bin/Plot_XX.pl ] to Plot the LDdecay
[b20223040323@admin2 test5]$ PopLDdecay -InVCF outcome.vcf -OutStat sun.stat.gz -SubPop sun.list
the Number of subPop samples[found in VCF] is 10
Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :3423
##begin pair-wise R^2 cal. after filter Remain SNP Number :     43219
#% number bin is        433
1%......-->100%.......          ALL done
Used [perl  ../bin/Plot_XX.pl ] to Plot the LDdecay
[b20223040323@admin2 test5]$ ls
dor.list  dor.stat.gz  gmm.list  gmm.stat.gz  outcome.vcf  sun.list  sun.stat.gz

 。

 

009、可视化

[b20223040323@admin2 test5]$ ls
dor.list  dor.stat.gz  gmm.list  gmm.stat.gz  multi.list  outcome.vcf  sun.list  sun.stat.gz
[b20223040323@admin2 test5]$ cat multi.list      ## 准备一个配置文件
dor.stat.gz     dor
gmm.stat.gz     gmm
sun.stat.gz     sun
[b20223040323@admin2 test5]$ Plot_MultiPop.pl -inList multi.list --out result_pig -bin1 10 -bin2 500      ## 绘图
null device
          1
null device
          1
[b20223040323@admin2 test5]$ ls
dor.list     gmm.list     multi.list   result_pig.dor  result_pig.pdf  result_pig.sun  sun.stat.gz
dor.stat.gz  gmm.stat.gz  outcome.vcf  result_pig.gmm  result_pig.png  sun.list

 .

备用参数：

01、Plot_MultiPop.pl -inList multi.list --out result_pig -bin1 10 -bin2 100 -break 100

02、Plot_MultiPop.pl -inList multi.list --out result_pig -bin1 20 -bin2 50 -break 1000

绘图结果：

 。

 

ref：

01、https://cloud.tencent.com/developer/article/1677015