How to view plink *.ld output
Hello,
I am a newbie in this avenue and I have just managed to generate some population sequencing data. I have generated the vcf files using Unified Genotyper (GATK) and then converted the vcf into plink . I did a pairwise LD matrix analysis and have the *.ld data sitting but I have no way to visualize it.
I tried Haploview but since my data is not human genome data, it spits out errors for chromosome number (3R in my case).
Would anyone be able to help me with visualizing this data please? My honours thesis depends upon it.
~Rahul.
I am a newbie in this avenue and I have just managed to generate some population sequencing data. I have generated the vcf files using Unified Genotyper (GATK) and then converted the vcf into plink . I did a pairwise LD matrix analysis and have the *.ld data sitting but I have no way to visualize it.
I tried Haploview but since my data is not human genome data, it spits out errors for chromosome number (3R in my case).
Would anyone be able to help me with visualizing this data please? My honours thesis depends upon it.
~Rahul.