wxs_pipeline

This pipeline takes arbitrary numbers of W[EG]S samples in BAM, or FASTQ format to create single-sample BAMs, gVCFs, VCFs, and a joint-genotyped VCF at the end, using the GATK Best Practices. The pipeline is currently configured to only support hg38 or GRCh37.

Requirements:

1. Install conda.
2. Install snakemake.
3. Install cookiecutter.
4. (Recommended): Initialize snakemake cluster profile.
5. Create an SSH key and configure github to use it.

6. Copy this repository with cookiecutter git+ssh://git@github.com/Gleeson-Lab/wxs_pipeline.git

Configuration:

Please see deploying the pipeline for more information.