vatools
Link to section 'Introduction' of 'vatools' Introduction
VAtools is a python package that includes several tools to annotate VCF files with data from other tools.
Docker hub: https://hub.docker.com/r/griffithlab/vatools
Home page: https://vatools.readthedocs.io/en/latest/
Link to section 'Versions' of 'vatools' Versions
- 5.0.1
Link to section 'Commands' of 'vatools' Commands
- ref-transcript-mismatch-reporter
- transform-split-values
- vcf-expression-annotator
- vcf-genotype-annotator
- vcf-info-annotator
- vcf-readcount-annotator
- vep-annotation-reporter
Link to section 'Module' of 'vatools' Module
You can load the modules by:
module load biocontainers
module load vatools
Link to section 'Example job' of 'vatools' Example job
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>