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.

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

usage: vep-annotation-reporter [-h] [-t INPUT_TSV] [-o OUTPUT_TSV]
                               input_vcf vep_fields [vep_fields ...]

positional arguments:
  input_vcf             The VCF file with VEP annotations to report.
  vep_fields            The VEP fields to report.

optional arguments:
  -h, --help            show this help message and exit
  -t INPUT_TSV, --input_tsv INPUT_TSV
                        A TSV report file to add VEP annotations to. Required
                        columns are CHROM, POS, REF, ALT. These are used to
                        match each TSV entry to a VCF entry. Must be tab-
                        delimited.
  -o OUTPUT_TSV, --output-tsv OUTPUT_TSV
                        Path to write the output report TSV file. If not
                        provided, the output TSV will be written next to the
                        input VCF with a .tsv file ending.

Example Command

vep-annotation-reporter input.vcf Consequence SYMBOL Feature -t input.tsv -o output.tsv