|FastQTL(1)||General Commands Manual||FastQTL(1)|
NAME¶FastQTL - Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
DESCRIPTION¶The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs) which are significantly associated with various molecular phenotypes (i.e. expression of known genes, cytosine methylation levels, etc). It performs scans for all possible phenotype-variant pairs in cis (i.e. variants located within a specific window around a phenotype). FastQTL implements a new permutation scheme (Beta approximation) to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels.
Print help about options.
- Silent mode on terminal.
- --seed arg (=1459232241)
- Random number generator seed. Useful to replicate runs of the software.
Input and Output files options¶
- -L, --log
- Screen output is copied in this file.
- -V, --vcf
- Genotypes in VCF format.
- -B, --bed
- Phenotypes in BED format.
- -C, --cov
- Covariates in TXT format.
- -G, --grp
- Phenotype groups in TXT format.
- -O, --out
- Output file.
Exclusion and Inclusion files options¶
- List of samples to exclude.
- List of samples to include.
- List of sites to exclude.
- List of sites to include.
- List of phenotypes to exclude.
- List of phenotypes to include.
- List of covariates to exclude.
- List of covariates to include.
- To perform quantile normalization on the phenotype quantifications to make them normally distributed. Implemented as the rntransform function of the GenABEL package.
- -W, --window
- Cis-window size. Default values is 1Mb (1e6). It means that all variants within 1e6 bp of the phenotype location (e.g. TSS) is analyzed.
- -T, --threshold
- To filter out all phenotype-variant pairs with a p-value above the specified threshold in the output of a nominal pass.
- -P, --permute
- Permutation pass to calculate corrected p-values for molecular phenotypes.
- Permutation sequence.
- Map best QTL candidates per molecular phenotype.
- Scan full cis-window to discover independent signals.
- Test for interactions with variable specified in file.
- -K, --chunk
- Specify which chunk needs to be processed.
- Generates all commands.
- -R, --region
- Region of interest.
EXAMPLE¶for c in $(seq 1 256); do fastQTL --vcf genotypes.vcf.gz --bed phenotypes.bed.gz --chunk $c 256 --permute 1000 --out results.$c.txt.gz
zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz
AUTHOR¶FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis.
This manual page was written by Dylan Aïssi <email@example.com>, for the Debian project (but may be used by others).