HLA and Haploview

Question

[samuelkyobe]

How can I use haploview to calculate and visualize HLA data linkage disequilibrium, I am completely stuck.

Answer 1

[Charles Warden]

While there may be advantages to visualizing the HLA region in Haploview, I would typically use an alternate set of references for analyzing the individual HLA genes.

So, I apologize that this doesn't directly answer your question, but it is possible there may be additional complications with this region.

For example, you may want to take a look at this discussion:

hg38 Ig regions

Answer 2

[samuelkyobe]

Thank you Charles. Do you recommend another tool.

[Charles Warden]

To be honest, I am not sure if I have created a plot for Haploview.

However, I describe some analysis of my HLA genes here:

http://cdwscience.blogspot.com/2019/08/predicting-hla-types-for-array-and-high.html

Also, I think you may want to move this question as a comment on my answer (rather than a separate answer). There are some moderation options, but I think repeating the question and deleting the answer may be the most effective (since you don't want to move a comment to an answer, or move an answer to a comment on the original question).