# mvgwas-nf [](http://nextflow.io) [](https://github.com/guigolab/sqtlseeker2-nf/actions/workflows/ci.yaml) A pipeline for multi-trait genome-wide association studies (GWAS) using [MANTA](https://github.com/dgarrimar/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](http://www.nextflow.io) as the execution backend. Please check [Nextflow documentation](http://www.nextflow.io/docs/latest/index.html) for more information. ## Requirements - Unix-like operating system (Linux, MacOS, etc.) - Java 8 or later - [Docker](https://www.docker.com/) (v1.10.0 or later) or [Singularity](http://singularity.lbl.gov) (v2.5.0 or later) ## Quickstart (~2 min) 1. Install Nextflow: ``` curl -fsSL get.nextflow.io | bash ``` 2. 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: * **Genotypes.** [bgzip](http://www.htslib.org/doc/bgzip.html)-compressed and indexed [VCF](https://samtools.github.io/hts-specs/VCFv4.3.pdf) genotype file. * **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](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`: chromosome * `POS`: position * `ID`: variant ID * `REF`: reference allele * `ALT`: alternative allele * `F`: pseudo-F statistic * `R2`: fraction of variance explained by the variant * `P`: 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](https://doi.org/10.1101/2022.06.06.493041)