elbecerrasoto / variants

Variant Calling Snakemake Pipeline

Variants

v0.2.0

Description

Variant Calling snakemake pipeline used at DeMoraes Lab.

It downloads a bacterial reference genome, and uses bowtie2, samtools and varscan to call variants.

Quick Usage

Style 1: using config/config.yaml

Edit config/config.yaml and then run.

snakemake --use-conda --cores all

Style 2: command line arguments

Specify configuration directly on the command line.

snakemake --cores all --use-conda --config\
    reference_id=GCA_013166975.1\
    input=input.tsv\
    results=results/

Generate report

snakemake --report report.zip

Inputs

The input is a tsv file with no headers and the following columns:

1. Sample name
2. Forward reads paths
3. Reverse reads paths

A script is provided to generate this file, to run it.

scripts/generate_input.py --mark1 _R1 --mark2 _R2 tests/data/

The generated file can then be manually edited, for further customization.

Outputs

The main output is a tsv of the variants, one file per sample.

Prerequisites

• An Anaconda Distribution
  • I recommended using miniforge
  • This README uses mamba, but substitute by conda if appropiatly.

Installation

git clone 'https://github.com/elbecerrasoto/variants'
cd variants

mamba env create
mamba activate variants

To test the installation.

make test

Usage

The pipeline uses the snakemake conventions, so you can edit the config file at config/config.yaml, and then run:

• snakemake --cores all --use-conda

TODO for v0.2.0

• Use "all" for bowtie cores
• Update readme
• Simplify config
• Simplify input files
• Log generation
• Script for suggesting input

TODO for future releases

• Workflow catalog standards

Issues

bowtie2 uses libcrypt.so.1 you can install it on manjaro like this:

• sudo pacman -S core/libxcrypt-compat