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
--local-cis- Considers SNPs around transcript as cis (instead of whole chromosome)
--radius [default=1000] arg- Size (in KB) around transcript considered cis
--full- Computes pairwise (including trans-trans) interactions
--TF- 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
Help
--help- Displays this screen
Example Usage
./iqtl --bfile plinkBfile --iqtl --transcript-matrix transcript.matrix --coordinates transcripts.bed --local-cis --out example