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).
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
Would anyone be able to help me with visualizing this data please? My honours thesis depends upon it.
![Frown](https://www.seqanswers.com/core/images/smilies/frown.png)
~Rahul.