Plotting linkage equilibrium results

Question

[tarek.mohamed]

Hi All ,

I did a LD analysis using a combination of bedtools, vcftools, and plink. I had 9000 SNPs distributed across 4 different genes which I did LD analysis for. Now I have LD analysis result (plink.ld) file. I want to view the analysis graphically, which tool do you recommend?

[tmm447@quser11 g1k_data_files]$ head plink.ld

CHR_A         BP_A         SNP_A  CHR_B         BP_B         SNP_B           R2           DP 
 6    160543123     rs1867351      6    160543148    rs12208357    0.0215633            1 
 6    160543123     rs1867351      6    160543229    rs55918055   0.00124509            1 
 6    160543123     rs1867351      6    160543562      rs461473    0.0291014            1 
 6    160543123     rs1867351      6    160543610     rs4709400            1            1 
 6    160543123     rs1867351      6    160543934    rs62440864     0.815385            1 
 6    160543123     rs1867351      6    160544680   rs192748353   0.00124509            1 
 6    160543123     rs1867351      6    160544961    rs73025537    0.0201052            1 
 6    160543123     rs1867351      6    160545046   rs111909590   0.00635448            1 
 6    160543123     rs1867351      6    160545394      rs463599    0.0403996            1

Thanks Tarek

Answer 1

[Hussain Ather]

If you want to use python, then matplotlib and seaborn might be helpful.