VCF Annotation Tools (VAtools)

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

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 the data from several expression tools’ output files to the VCF INFO column. Supported tools are StringTie, Kallisto, and Cufflinks. There also is a custom option to annotate with data from any tab-delimited file.

vcf-info-annotator

A tool that will add data from a tab-delimited file to any user-specified field in the VCF INFO column.

vep-annotation-reporter

A tool to create a tab-delimited (TSV) file of variants in a VCF and their VEP annotations.