Vatools

Introduction

VAtools is a python package that includes several tools to annotate VCF files with data from other tools.

For more information, please check:
Docker hub: https://hub.docker.com/r/griffithlab/vatools
Home page: https://vatools.readthedocs.io/en/latest/

Versions

  • 5.0.1

Commands

  • ref-transcript-mismatch-reporter

  • transform-split-values

  • vcf-expression-annotator

  • vcf-genotype-annotator

  • vcf-info-annotator

  • vcf-readcount-annotator

  • vep-annotation-reporter

Module

You can load the modules by:

module load biocontainers
module load vatools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run vatools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vatools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers vatools

vcf-readcount-annotator <input_vcf> <snv_bam_readcount_file> <DNA| RNA> \
            -s <sample_name> -t snv -o <snv_annotated_vcf>