mvgwas-nf
A pipeline for multi-trait genome-wide association studies (GWAS) using MANTA.
The pipeline performs the following analysis steps:
- Split genotype file
- Preprocess phenotype and covariate data
- Test for association between phenotypes and genetic variants
- Collect summary statistics
The pipeline uses Nextflow as the execution backend. Please check Nextflow documentation for more information.
Requirements
- Unix-like operating system (Linux, MacOS, etc.)
- Java 8 or later
- Docker (v1.10.0 or later) or Singularity (v2.5.0 or later)
Quickstart (~2 min)
-
Install Nextflow:
curl -fsSL get.nextflow.io | bash
-
Make a test run:
nextflow run dgarrimar/mvgwas-nf -with-docker
Notes: move the nextflow
executable to a directory in your $PATH
. Set -with-singularity
to use Singularity instead of Docker.
(*) Alternatively you can clone this repository:
git clone https://github.com/dgarrimar/mvgwas-nf
cd mvgwas-nf
nextflow run mvgwas.nf -with-docker
Pipeline usage
Launching the pipeline with the --help
parameter shows the help message:
nextflow run mvgwas.nf --help
N E X T F L O W ~ version 20.04.1
Launching `mvgwas.nf` [amazing_roentgen] - revision: 56125073b7
mvgwas-nf: A pipeline for multivariate Genome-Wide Association Studies
==============================================================================================
Performs multi-trait GWAS using using MANTA (https://github.com/dgarrimar/manta)
Usage:
nextflow run mvgwas.nf [options]
Parameters:
--pheno PHENOTYPES phenotype file
--geno GENOTYPES indexed genotype VCF file
--cov COVARIATES covariate file
--l VARIANTS/CHUNK variants tested per chunk (default: 10000)
--t TRANSFOMATION phenotype transformation: none, sqrt, log (default: none)
--i INTERACTION test for interaction with a covariate: none, (default: none)
--ng INDIVIDUALS/GENOTYPE minimum number of individuals per genotype group (default: 10)
--dir DIRECTORY output directory (default: result)
--out OUTPUT output file (default: mvgwas.tsv)
Input files and format
mvgwas-nf
requires the following input files:
-
Phenotypes. Tab-separated file with phenotype measurements (quantitative) for each sample (i.e. n samples x q phenotypes). The first column should contain sample IDs. Columns should be named.
-
Covariates. Tab-separated file with covariate measurements (quantitative or categorical) for each sample (i.e. n samples x k covariates). The first column should contain sample IDs. Columns should be named.
Example data is available for the test run.
Pipeline results
An output text file containing the multi-trait GWAS summary statistics (default: ./result/mvgwas.tsv
), with the following information:
CHR
: chromosomePOS
: positionID
: variant IDREF
: reference alleleALT
: alternative alleleF
: pseudo-F statisticR2
: fraction of variance explained by the variantP
: P-value
The output folder and file names can be modified with the --dir
and --out
parameters, respectively.
Cite mvgwas-nf
If you find mvgwas-nf
useful in your research please cite the related publication:
Garrido-Martín, D., Calvo, M., Reverter, F., Guigó, R. A fast non-parametric test of association for multiple traits. bioRxiv (2022). https://doi.org/10.1101/2022.06.06.493041
Version History
master @ aaa979d (earliest) Created 15th Feb 2023 at 11:58 by Diego Garrido-Martín
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Created: 15th Feb 2023 at 11:58
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