HLA and Haploview
How can I use haploview to calculate and visualize HLA data linkage disequilibrium, I am completely stuck.
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
Thank you Charles. Do you recommend another tool.
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