Variant Annotation Integrator
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Using the Variant Annotation Integrator
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Introduction
The Variant Annotation Integrator (VAI) is a research tool for associating
annotations from the UCSC database with your uploaded set of variant calls.
It uses gene annotations to predict functional effects of variants on transcripts.
For example, a variant might be located in the coding sequence
of one transcript, but in the intron of an alternatively spliced transcript
of the same gene; the VAI will return the predicted functional effect
for each transcript. The VAI can optionally add several other
types of relevant information: the dbSNP identifier if the variant
is found in
dbSNP,
protein damage scores for missense variants from the
Database of Non-synonymous Functional Predictions (dbNSFP),
and conservation scores computed from multi-species alignments.
The VAI can optionally filter results to retain only specific functional
effect categories, variant properties and multi-species conservation status.
NOTE:
The VAI is only a research tool, meant to be used by those who have been
properly trained in the interpretation of genetic data,
and should never be used to make any kind of medical decision.
We urge users seeking information about a personal medical or genetic
condition to consult with a qualified physician for diagnosis and for
answers to personal questions.
Submitting your variant calls
In order to use the VAI, you must provide variant calls in either the
Personal Genome SNP (pgSnp) or
VCF format.
pgSnp-formatted variants may be uploaded as a
Custom Track.
Compressed and indexed VCF files must be on a web server (HTTP, HTTPS or FTP)
and configured as Custom Tracks, or if you happen to have a
Track Hub,
as hub tracks.
Protein-coding gene transcript effect predictions
Any gene prediction track in the UCSC Genome Browser database or in a track hub
can be selected as the VAI's source of transcript annotations for prediction
of functional effects.
Sequence Ontology (SO) terms are used to describe the effect
of each variant on genes in terms of transcript structure as follows:
SO term | description |
intergenic_variant |
A sequence variant located in the intergenic region, between genes. |
upstream_gene_variant |
A sequence variant located 5' of a gene. (VAI searches within 5,000 bases.) |
downstream_gene_variant |
A sequence variant located 3' of a gene. (VAI searches within 5,000 bases.) |
5_prime_UTR_variant |
A variant located in the 5' untranslated region (UTR) of a gene. |
3_prime_UTR_variant |
A variant located in the 3' untranslated region (UTR) of a gene. |
synonymous_variant |
A sequence variant where there is no resulting change to the encoded amino acid. |
missense_variant |
A sequence variant, that changes one or more bases, resulting in a
different amino acid sequence but where the length is preserved. |
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