The HaploHammer pipeline parses haplotypes from VCF files. The purpose of this Snakemake wrapper is to facilitate the use of HaploHammer for population-level VCF files and to eliminate the need to install any dependencies, including python 2.
Before running the pipeline, you must have the following installed:
To install the pipeline, simply clone the repository:
git clone https://github.com/Kobie-Kirven/HaploHammer-Snakemake.git
Before running the pipeline, you must first edit the config file and fill in the fields. NOTE: All paths must be absolute paths (meaning they must start with a /).
Example:
# VCF file to be analyzed
vcf: /Users/path/to/vcf/file.vcf.gz
Once the config file is filled out, you can run the pipeline using the following command:
snakemake --use-conda --conda-frontend conda --cores <number of cores>
And that's it! The pipeline will run and output will be an allele_matrix.csv file in the specified output directory.