Calculate Ld Between 2 Loci

Question

[Sander Timmer]

I know there are several ways of calculating LDs using tools like plink when using genotyping data. In my case I've several different loci on the genome that show some sort of interaction. Some of these might have SNPs thus I could use the SNPs LD as a measure though in many other cases I don't have SNPs in the regions of interest. I assume that in these cases some sort of estimation has to be done which is fine for what I want to-do with my data.

Hence, is there a simple way to get LDs between 2 regions on the genome. Samples are CEU and are part of HapMap/1,000 Genomes so data is plentiful. Is there maybe a simple webservice which I could use that already has this kind of information pre-computed or compute on the fly?

Answer 1

[Ryan D]

There is a tool called GLIDERS which has pairwise LD calculated between all SNPs in the genome beyond the 500kb limit of SNAP. http://www.sanger.ac.uk/resources/software/gliders/ has all r2>0.3 calculated for all pairwise combinations. It also does inter-chromosomal LD estimates. It uses phase 2 and 3 HapMap genotypes to calculate LD and only SNPs with MAF > 0.05.

Of course, this is to do a quick search. You're better off using 1000 genomes data and your population of interest. I use the following commands to do it specifically for the Asian population.

tabix -fh ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr4.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz 4:151890286-154092741 > ~/genotypes.vcf 
./vcftools_0.1.7/cpp/vcftools --vcf ~/genotypes.vcf --plink --out plinkformat 
plink --bfile plinkformat --keep ~/CNV/REFERENCE_CNVS/1kg_asn.lst --make-bed --out asn &
plink --bfile asn --ld-snp rsXXX --ld-window-kb 2000 --ld-window 99999 --ld-window-r2 0 --out asn

In the above commands the 1kg_asn.lst is a list of the Asian samples in 1000 Genomes and rsXXX is whatever rs# you choose to use. You can use any of PLINK's LD commands.

[Adam]

vcftools also has the --hap-r2 and --geno-r2 options for calculating LD without first converting to PLINK.

Answer 2

[1234Jc4321]

http://www.broadinstitute.org/mpg/snap/ldsearch.php

This link might be helpful.