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
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Clone the repository
git clone https://github.com/lumc-pgx/phasing.git
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Change to the phasing directory
cd phasing
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Create a conda environment for running the pipeline
conda env create -n phasing -f environment.yaml
Pipeline configuration settings can be altered by editing config.yaml.
- Activate the conda environment
source activate phasing
- Run the Snakefile using snakemake