Question: Automatic Ld Plot For Multiples Snps On Different Chromosome
0
gravatar for Maxime Lamontagne
6.5 years ago by
Québec
Maxime Lamontagne2.1k wrote:

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

ld haploview • 1.7k views
ADD COMMENTlink written 6.5 years ago by Maxime Lamontagne2.1k
0
gravatar for Maxime Lamontagne
6.5 years ago by
Québec
Maxime Lamontagne2.1k wrote:

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.

ADD COMMENTlink written 6.5 years ago by Maxime Lamontagne2.1k
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