Automatic Ld Plot For Multiples Snps On Different Chromosome

Question

[Maxime Lamontagne]

Hi,

I have a list of SNPs (n = 100). They are located on different chromosomes and I want to check if some SNPs are in LD.

I don't have any genotypes data for these SNPs.

Thanks

Answer 1

[Maxime Lamontagne]

Finally, I was able to do it with a little imagination and a lot of bash code.

Step 1: Find genomic location of each SNP with a file downloaded from UCSC.

Step 2: Extract genotype from 1000 Genome Project for each SNP in PLINK format. Merge SNP of the same chromosome.

Step 3: Make LD plot with command line.