Genofinder
A nextflow pipeline to extract SNPs and regions from imputed genotypes.
Quick Start
-
Install Nextflow (>=21.04.0)
-
Run the pipeline on a test dataset
nextflow run main.nf -profile test,development
Parameters
Required parameters
| Option | Value | Description |
|---|---|---|
project |
my-project-name | Name of the project |
genotypes_array |
/path/to/allChrs.{bim,bed,fam} | Path to the array genotypes (single merged file in plink format). |
genotypes_imputed |
/path/to/vcf/*vcf.gz or /path/to/bgen/*bgen | Path to imputed genotypes in VCF or BGEN format) |
genotypes_imputed_format |
vcf or bgen | Input file format of imputed genotypes |
genotypes_build |
hg19 or hg38 | Imputed genotypes build format |
queries |
/path/to/query-file.txt | File with queries (line by line) |
Development
docker build -t lukfor/genofinder:latest . # don't ignore the dot
nextflow run main.nf -profile test,development
License
genofinder is MIT Licensed.
Contact
If you have any questions about this pipeline please contact