Friday, August 23, 2013

Fwd: [genome-announce] Variant Annotation Integrator

variant effect predictors and annotators are key to NGS analysis, nice addition!

Fwd: please follow footer link

[genome-announce] Variant Annotation Integrator: "Hello all,


In order to assist researchers in annotating and prioritizing thousands

of variant calls from sequencing projects, we have developed the Variant

Annotation Integrator (VAI). Given a set of variants uploaded as a

custom track (in either pgSnp or VCF format), the VAI will return the

predicted functional effect (e.g., synonymous, missense, frameshift,

intronic) for each variant. The VAI can optionally add several other

types of relevant information, including: 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 also

offers filters to help narrow down results to the most interesting variants.


Future releases of the VAI will include more input/upload options,

output formats, and annotation options, and a way to add information

from any track in the Genome Browser, including custom tracks.


There are two ways to navigate to the VAI: (1) From the 'Tools' menu,

follow the 'Variant Annotation Integrator' link. (2) After uploading a

custom track, hit the 'go to variant annotation integrator' button. The

user's guide is at the bottom of the page, under 'Using the Variant

Annotation Integrator.'


As always, we welcome questions and feedback on our public mailing list:
genome@soe.ucsc.edu.


--

Brooke Rhead

UCSC Genome Bioinformatics Group


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(Via UCSC-announce.)