VEP Annotation Reporter ======================= VEP annotations in a VCF can be difficult to read and interpret. We developed the VEP Annotation Report to aid in converting VEP annotation fields to a human-readable report. The VEP Annotation Reporter will create a tab-delimited (TSV) file of variants in a VCF and their VEP annotations. The VEP fields to add to the output TSV are specified by listing one or more VEP annotation field identifiers as positional parameters after the input VCF. The VEP fields of an input VCF can be identified by inspecting the ``Description`` field of the ``CSQ`` ``INFO`` header in the VCF. Everything after ``Format:`` is a field available in the VCF (delimited by ``|``). If a variant is annotate with multiple transcript consequences by VEP then the values for all transcript annotation will be returned as comma-separated values. This is the default behavior unless VEP was run with one of the ``--flag_pick`` options, all possible transcript consequences will be reported by VEP but only one of these consequences will be picked by VEP as the "best" consequence. This is denoted in the ``PICK`` field. If this field is available, then the values for that transcript will be reported. For some variants, VCFs annotated with the ``PICK`` field might not report any of the consequences as picked. In that case, the values for all transcript consequences are reported. VEP annotations can also be added to an existing TSV with variant information by using the ``--input-tsv`` option. In order to match the variants in the TSV to the variants in the VCF, the existing TSV file will need to contain columns with the headers ``CHROM``, ``POS``, ``REF``, and ``ALT`` where the values match the VCF ``CHROM``, ``POS``, ``REF``, and ``ALT`` values. By default the output TSV will be written to a ``.tsv`` file next to your input VCF file. You can set a different output file using the ``--output-tsv`` parameter. Usage ----- .. program-output:: vep-annotation-reporter -h Example Command --------------- .. code-block:: none vep-annotation-reporter input.vcf Consequence SYMBOL Feature -t input.tsv -o output.tsv