https://github.com/griffithlab/vatools

A set of tools to annotate VCF files with expression and readcount data
https://github.com/griffithlab/vatools

Last synced: 9 months ago
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A set of tools to annotate VCF files with expression and readcount data

• Host: GitHub
• URL: https://github.com/griffithlab/vatools
• Owner: griffithlab
• License: mit
• Created: 2018-04-23T19:14:19.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2025-03-04T15:14:04.000Z (over 1 year ago)
• Last Synced: 2025-09-06T06:03:28.171Z (10 months ago)
• Language: Python
• Homepage: http://www.vatools.org
• Size: 38.8 MB
• Stars: 29
• Watchers: 16
• Forks: 13
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# VCF Annotation Tools (VAtools)

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.

## Documentation

Please see [vatools.org](http://vatools.org) for the full documentation.

## Install

`pip install vatools`