.. VAtools  documentation master file, created by
   sphinx-quickstart on Wed Aug  8 09:54:20 2018.
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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.

**vcf-genotype-annotator**
    A tool to add a new sample to an existing VCF file or fill in the GT field
    for an existing sample in a VCF.

**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.

.. toctree::
   :maxdepth: 1

   vcf_readcount_annotator
   vcf_expression_annotator
   vcf_info_annotator
   vcf_genotype_annotator
   vep_annotation_reporter
   ref_transcript_mismatch_reporter
   transform_split_values
   install
   license
   contact