VCF Annotation Tools (VAtools)
VCF Annotation Tools is a python package that includes several tools to annotate VCF files with data from other tools.
A tool that will add the data from bam-readcount files to the VCF sample column.
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.
A tool that will add data from a tab-delimited file to any user-specified field in the VCF INFO column.
Please see vatools.org for the full documentation.
pip install vcf-annotation-tools