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