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Variant Effect Predictor Custom annotations


The VEP script can integrate custom annotation from standard format files into your results by using the --custom flag.

These files may be hosted locally or remotely, with no limit to the number or size of the files. The files must be indexed using the tabix utility (BED, GFF, GTF, VCF); bigWig files contain their own indices. Users should note that the VEP will only look for overlaps (both exact and inexact) with these annotations; for example, any sequence in a GTF file will not be taken into account.

Annotations appear as key=value pairs in the Extra column of the VEP output; they will also appear in the INFO column if using VCF format output. The value for a particular annotation is defined as the identifier for each feature; if not available, an identifier derived from the coordinates of the annotation is used. Annotations will appear in each line of output for the variant where multiple lines exist.

Data formats

The VEP supports the following formats:

  • BED : a simple tab-delimited format containing 3-12 columns of data. The first 3 columns contain the coordinates of the feature. If available, the VEP will use the 4th column of the file as the identifier of the feature.
  • GFF : a format for describing genes and other features. If available, the VEP will use the "ID" field as the identifier of this feature.
  • GTF : treated in an identical manner to GFF.
  • VCF : a format used to describe genomic variants. The VEP will use the 3rd column of the file as the identifier.
  • bigWig : a format for storage of dense continuous data. The VEP uses the value for the given position as the "identifier". Note that bigWig files contain their own indices, and do not need to be indexed by tabix.

Any other files can be easily converted to be compatible with the VEP; the easiest format to produce is a BED-like file containing coordinates and an (optional) identifier:

chr1    10000    11000    Feature1
chr3    25000    26000    Feature2
chrX    99000    99001    Feature3

Chromosomes can be denoted by either e.g. "chr7" or "7", "chrX" or "X".


Preparing files

Custom annotation files must be prepared in a particular way in order to work with tabix and therefore with the VEP. Files must be sorted in chromosome and position order, compressed using bgzip and finally indexed using tabix. Here is an example of that process for a BED file:

sort -k1,1 -k2,2n -k3,3n myData.bed | bgzip > myData.bed.gz
tabix -p bed myData.bed.gz

The tabix utility has several preset filetypes that it can process, and it can also process any arbitrary filetype containing at least a chromosome and position column. See the documentation for details.

If you are going to use the file remotely (i.e. over HTTP or FTP protocol), you should ensure the file is world-readable on your server.


Options

Each custom file that you configure the VEP to use can be configured. Beyond the filepath, there are further options, each of which is specified in a comma-separated list, for example:

perl variant_effect_predictor.pl -custom myFeatures.gff.gz,myFeatures,gff,overlap,0
perl variant_effect_predictor.pl -custom frequencies.bw,Frequency,bigwig,exact,0
perl variant_effect_predictor.pl -custom http://www.myserver.com/data/myPhenotypes.bed.gz,Phenotype,bed,exact,1

The options are as follows:

  • Filename : The path to the file. For tabix indexed files, the VEP will check that both the file and the corresponding .tbi file exist. For remote files, the VEP will check that the tabix index is accessible on startup.
  • Short name : A name for the annotation that will appear as the key in the key=value pairs in the results. If not defined, this will default to e.g. "Custom1" for the first set of annotation added.
  • File type : One of "bed", "gff", "gtf", "vcf", "bigwig". If not specified, the VEP assumes the file is BED format.
  • Annotation type : One of "exact", "overlap". When using "exact" only annotations whose coordinates match exactly those of the variant will be reported. This would be suitable for position specific information such as conservation scores, allele frequencies or phenotype information. Using "overlap", any annotation that overlaps the variant by even 1bp will be reported.
  • Force report coordinates : One of "0" or "1" (if left blank assumed to be "0") - if set to "1", this forces the VEP to output the coordinates of an overlapping custom feature instead of any found identifier (or value in the case of bigWig) field. If set to "0" (the default), the VEP will output the identifier field if one is found; if none is found, then the coordinates are used instead.
  • VCF fields : if any field names are specified that are found in the info field of the VCF, these will also be added as custom annotations. Only applies when using VCF format custom files.

All options (apart from the filename) are optional and their absence will invoke the default behaviour.


Using remote files

The tabix utility makes it possible to read annotation files from remote locations, for example over HTTP or FTP protocols. In order to do this, the .tbi index file is downloaded locally (to the current working directory) when the VEP is run. From this point on, only the portions of data requested by the script (i.e. those overlapping the variants in your input file) are downloaded. Users should be aware, however, that it is still possible to cause problems with network traffic in this manner by requesting data for a large number of variants. Users with large amounts of data should download the annotation file locally rather than risk causing any issues!

bigWig files can also be used remotely in the same way as tabix-indexed files, although less stringent checks are carried out on VEP startup. Furthermore, when using bigWig files, the VEP generates temporary files that by default are written to the /tmp/ directory - to override this, use the --tmpdir /my/tmp/dir flag.


Annotating existing results

It is possible to add custom annotation to existing VEP results files. To do this, you need to specify the --no_consequence option, and provide your VEP output file as the input file for the script. The script should auto-detect the format of the file; if it does not, you can force it to read the file as VEP output using --format vep.