PGX module

This workflow is designed to generate sample-specific report with clinical guidelines dependent on variants detected in a Genomic Medicine Sweden sequencing panel.

It is designed to be coupled to an existing pipeline and need to be given the location of analysis ready bam files, path to which is specified in data/example_config.

Setup

Set paths in data/example_congif.yaml for reference_fasta and dbsnp to suitable files, as well as bam_location to input-pattern to bamfiles. specify the samples and sequencerun desired.

If using singularity with snakemake please run script envs/get_containers.sh

This was tested using:

• Snakemake 5.6.0
• Hg19 reference genome
• dbsnp build 138