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¶
usage: vep-annotation-reporter [-h] [-t INPUT_TSV] [-o OUTPUT_TSV]
input_vcf vep_fields [vep_fields ...]
A tool to create a tab-delimited (TSV) file of variants in a VCF and their VEP
annotations.
positional arguments:
input_vcf The VCF file with VEP annotations to report.
vep_fields The VEP fields to report. Takes a space-separated list
of fields. Example: Consequence SYMBOL Feature
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