VAtools (VCF Annotation Tools) is a python package for easy manipulation of genomic data stored in the common VCF format
vcf-readcount-annotator
A tool that will add the data from bam-readcount files to the VCF sample column.
vcf-expression-annotator
A tool that will add gene expression data to the VCF FORMAT column on a per-sample basis. StringTie, Kallisto, and Cufflinks outputs are supported natively, or there is a custom option to annotate with data from any tab-delimited file.
vcf-info-annotator
A general-purpose tool that will add data from a tab-delimited file to any user-specified field in the VCF INFO column.
vcf-genotype-annotator
A tool to add a new sample to an existing VCF file.
vep-annotation-reporter
A tool to extract human-readable variant annotation data (in TSV format) from a VEP-annotated VCF.
ref-transcript-mismatch-reporter
A tool to identify 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).
transform-split-values
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.
pip install vatools
VAtools is available as a Docker Image at DockerHub griffithlab/vatools.
