sequana-variant-calling 0.8.0

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_variant_calling

Usage

sequana_pipelines_variant_calling --help
sequana_pipelines_variant_calling --input-directory DATAPATH --run-mode local --reference measles.fa
sequana_pipelines_variant_calling --input-directory DATAPATH --run-mode slurm --reference measles.fa

This creates a directory variant_calling. You just need to execute the pipeline:

cd variant_calling
snakemake -s variant_calling.rules --stats stats.txt

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters:

snakemake -s variant_calling.rules --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• bwa

• freebayes

• picard (picard-tools)

• sambamba

• samtools

• snpEff

Details

Snakemake variant calling pipeline is based on tutorial written by Erik Garrison. Input reads (paired or single) are mapped using bwa and sorted with sambamba-sort. PCR duplicates are marked with sambamba-markdup. Freebayes is used to detect SNPs and short INDELs. The INDEL realignment and base quality recalibration are not necessary with Freebayes. For more information, please refer to a post by Brad Chapman on minimal BAM preprocessing methods.

The pipeline provides an analysis of the mapping coverage using sequana coverage. It detects and characterises automatically low and high genome coverage regions.

Detected variants are annotated with SnpEff if a GenBank file is provided. The pipeline does the database building automatically. Although most of the species should be handled automatically, some special cases such as particular codon table will required edition of the snpeff configuration file.

Finally, joint calling is also available and can be switch on if desired.

Rules and configuration details