Fast Eqtl Analysis Tool

Question

[Purpleone]

I've got about 2M imputed SNPs and 35K gene expression probesets, and I'd like to identify all eQTL.

Running this under PLINK --linear is going to take a very long time, are there any specialized tools out there to handle this sort of data?

Answer 1

[brentp]

This just came out:

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

I've run it on 2.1million methylation probes * 40K expression probes * 200 individuals in about 26 hours.

[Sean Davis]

A bit off-topic, but if you end up with a blog post on the topic, let us all know.

[Andrey Shabalin]

Here is a blog post about this software: http://adairama.wordpress.com/2012/02/03/matrix-eqtl-ultra-fast-eqtl-analysis/

[Khader Shameer]

Looks neat, thanks for sharing.

Answer 2

[Sean Davis]

See here for a list. Not listed on that page is Vince Carey's GGTools package from Bioconductor which has infrastructure for doing eQTL analysis.

Answer 3

[Maxime Lamontagne]

Actually, you can do it with PLINK, But you need to make several --pheno files. After each run, you need to isolate only good p values. I don't recommend to keep all qassoc files because they are big. Actually, with 1 computer, you could do the analysis in 2 weeks.

Answer 4

[lkmklsmn]

Best EQTL package is MatrixEQTL! It's amazing. Trans eQTL (6k genes 2M SNPs) analysis can be done in 5-6 hours. Cis eQTL analysis under one hour.