Variant calling workflow

Calling of normalized hgvs variants for amplicon sequences

The variant calling workflow module performs the following operations:

• Creation of a reference fasta sequence for the targetted region.
• Alignment of amplicon sequences to the reference sequence.
• 'Calling' of normalized hgvs-like variants.

The pipeline outputs two files per barcode:

• A {barcode}.json file which contains the found variants per allele sequence
• A {barcode}.aln file which contains the alignments used for the variant calling

Requirements

• Conda/Miniconda

Installation

• Clone the repository

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

• Change to the variant_calling directory

  • cd variant_calling

• Create a conda environment for running the pipeline

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

Configuration

The pipeline configuration settings are specified in config.yaml.
Edit the configfile with run-specific paths and settings.

Execution

• Activate the conda environment
  • source activate variant_calling
• Run the pipeline using Snakemake