Pancov is a workflow that builds on the ARTIC-Pipeline (link) to improve nCoV-19 variant calling by aligning reads to a pangenomic variant graph.
This repository is a snakemake workflow that uses conda as a software versioning tool.
In order to run it you need to have a working conda installation as well as snakemake installed.
As an alternative to using conda yourself we provide a docker image that can be used which contains all conda environments.
To execute the workflow, simply edit the config.example.yaml and rename it to config.yaml.
Place the required input files in data/input.
For example your folder structure could be:
data/input/nCoV-2019.reference.fasta
data/input/run1/sample1.medaka.pass.vcf
data/input/run1/sample1.medaka.primertrimmed.rg.sorted.bam
data/input/run1/sample2.medaka.pass.vcf
data/input/run1/sample2.medaka.primertrimmed.rg.sorted.bam
Then run:
snakemake --use-conda --cores X
or to use the dockerized version:
snakemake --use-singularity --use-conda --cores X
where X is the amount of concurrent cores you want to utilize.
For a detailed description of the method refer to: [LINK TO PAPER]