I would like to perform linkage disequilibrium test for a number of SNPs. I am absolutely new to this field and would like to know what input file should be taken for my SNPs. I also would like to know the HapMap format for the LD test.
Kindly help me asap.
Hi Rini Chaturvedi,
If I understood the data correctly, you can use it to test linkage disequilibrium. However, I think Haploview has a feature to limit the LD calculations in a specific window by ignoring the pairwise comparisons farther than 500 Kb.
Even though, you might be able to perform the LD calculations if your SNP positions are more distant than 500Kb by setting the window to a higher value or zero (all comparisons).
Haploview accepts a lot of formats for our convenience, but I prefer to use the PLINK format because it is easier to generate from a VCF file and you also will be able to use the same input in other softwares.
I hope this answer helps you. Let us know if you have any questions about this answer by posting a message below.
Best,
Joao Paulo
Hi Joao Paulo,
Thank you so much for your help. I will try to generate the PLINK format and hope to get my work done.
Thanks.
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