VCF Annotation Tools 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.

vcf-genotype-annotator

A tool to add a new sample to an existing VCF file.

vep-annotation-reporter

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

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