Wednesday, July 24, 2013

Fwd: [genome-announce] Variant Annotation Integrator

Simple choice for NGS projects: Integrate or 'disintegrate' (mirror in DK)

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:

Brooke Rhead
UCSC Genome Bioinformatics Group

(Via UCSC-announce.)