Phasing

Creation of phased allele sequences

The phasing module generates phased and polished allele sequences:

• CCS sequences are used to partition the sequences into potential phases
• LAA is used to generate high quality consensus sequences for each phase
• Metrics and summaries are produced to aid with interpretation

Requirements

• Conda/Miniconda

Installation

• Clone the repository

  • git clone https://github.com/lumc-pgx/phasing.git

• Change to the phasing directory

  • cd phasing

• Create a conda environment for running the pipeline

  • conda env create -n phasing -f environment.yaml

Configuration

Pipeline configuration settings can be altered by editing config.yaml.

Execution

• Activate the conda environment
  • source activate phasing
• Run the Snakefile using snakemake