Pairwise linkage disequilibrium

Question

[ivenisec]

I have a file with hundreds of rsIDs in pairs. I want to test if each pair is in linkage disequilibrium. Is there a tool that can calculate all of them at the same time? My file looks like this: (the reference sequence is hg19)

rs4648356    rs6687680

rs227163      rs12407642

rs227163      rs10489448

rs616488      rs1755594

Thanks for the help!

[LauferVA]

in LD in what population? Do you also have a file with genotypes?

Answer 1

[reza.jabal]

This is a shut in the dark unless you'd like to check pairwise LD in one of the HapMap reference populations. The rest is relatively straightforward in Bioconductor:

> library(LDheatmap)
> data("CEUData")
> MyHeatmap <- LDheatmap(CEUSNP, CEUDist, LDmeasure = "r",
+ title = "Pairwise LD in r^2", add.map = TRUE,
+ SNP.name = c("rs4648356", "rs6687680"), color = grey.colors(20),
+ name = "myLDgrob", add.key = TRUE)

You can write a bash script to read from your snpList.file and pass it to the R. You may find this helpful!