VariantAnnotationTool
From Genecats
Revision as of 19:18, 18 January 2012 by AngieHinrichs (talk | contribs) (Template design doc for proposed Variant Annotation Tool, from Ann's suggestions (Redmine #6152), with some strawman contents)
Use cases
Novel variant calls from sequencing experiment
List of rs IDs
Implementation plan: who's going to do what?
Features
Like many existing tools, we will report the variants' effects on genes (splice-3, coding-non-synon etc.).
UCSC's major enhancements will be
- the incorporation of the many types of data in our database
- presentation of the results: not just loads of data, but also links to browser views
Input
- pgSnp
- VCF
- Other formats, e.g. outputs of popular NGS pipelines?
- 23andMe? :)
Output
- tab-separated file
- custom track in GB/TB
- intermediate level to summarize and filter findings
Interface
CGI
Main page
Form:
- paste/upload variants
- select annotation sources
- any track including custom tracks?
- select output format/presentation
- custom track in [Genome Browser | Table Browser]
- summary with filters
- go!
followed by brief how-to and link to more detailed doc.
Summary/Filters
Stats: #variants, #variants intersecting each annotation source (further broken down for protein-coding genes)
Form:
- Select annotation source
- Filters
- For protein-coding gene annotations: coding-non-synon, etc.
- For wiggle tracks: min/max threshold
- ...?
