VAtools (VCF Annotation Tools) is a python package for easy manipulation of genomic data stored in the common VCF format
A tool that will add the data from bam-readcount files to the VCF sample column. Writes depth, allele counts, and VAFs; optionally also writes detailed per-read quality metrics (mapping quality, base quality, strand counts, and more) as additional FORMAT fields.
A tool that will add the data from several expression tools’ output files to the VCF FORMAT column, on a per-sample basis. Directly supports outputs from StringTie, Kallisto, Cufflinks, or custom formats that you define.
A general-purpose tool that will add data from a tab-delimited file into VCF INFO fields. Supports mapping multiple TSV columns to multiple INFO fields in a single pass.
A tool to add a new sample to an existing VCF file or fill in the GT field for an existing sample in a VCF. Fills a need for genotype manipulation in VCFs that don’t contain one, which can cause errors in downstream tools.
VEP annotations in a VCF are condensed into a CSQ field that is meant to be machine-readable, and can be difficult for humans to read and interpret. The VEP Annotation Reporter extracts it into a human-readable report.
ref-transcript-mismatch-reporter
A tool to identify problematic variants in a VCF where the reference genome used to align and call variants doesn’t match the Ensembl reference transcript used by VEP for variant consequence annotations.
A tool that extracts and manipulates values from existing sample fields and outputs the results to a TSV file.
Please see vatools.org for the full documentation.
Install with pip
pip install vatools
Or with bioconda
conda install -c bioconda -c conda-forge vatools
VAtools is available as a Docker Image at DockerHub griffithlab/vatools.
