iqtl – a Linux command line tool for uncovering interactions between SNPs that regulate gene expression.

Command Line

iQTL is invoked with the command iqtl --iqtl and has the following command line options:

Required Input Files

--bfile arg
plink .bed/.bim/.fam file prefix containing SNPs
--transcript-matrix arg
Matrix of transcripts (rows) by individuals (columns)
--coordinates arg
File of CHR, BP Start, BP End, Transcript name (tab delimited)

Optional Commands

Considers SNPs around transcript as cis (instead of whole chromosome)
--radius [default=1000] arg
Size (in KB) around transcript considered cis
Computes pairwise (including trans-trans) interactions
Select SNPs in range of 1 or more transcription factors
--TF-radius [default=0] arg
Number of kilobases considered within TF radius
--TF-file arg
Select coordinates file different from default

Include Covariates

--covar arg
Plink covariate file format


Displays this screen

Example Usage

./iqtl --bfile plinkBfile --iqtl --transcript-matrix transcript.matrix --coordinates transcripts.bed --local-cis --out example