|
Geneticist Assistant is compatible
with data processed from all leading
next generation sequencing platforms
such as those from Ion Torrent and
Illumina. The program accepts standardized
BAM and VCF files, includes prediction
information from SIFT, PolyPhen2,
LRT and Mutation Taster as well as
conservation scores data from PhyloP,
GERP++, SiPhy and population frequencies
from ExAC, GnomAD, and Exome Variant
Server. Additionally, information
from proprietary custom databases
and from the COSMIC database of somatic
mutations are easily imported into
the workbench.
Sample’s
Variants: Example configuration
of variant table. Columns can be customized
to show the fields needed. Variant
pathogenicity is set by the user and
shown in other samples.
Geneticist Assistant software includes
valuable tools for variant filtering,
sample comparisons - including trio
and family comparisons - custom PDF
report design, and review of customizable
quality metrics.
Filtering:
The sample’s variants have been set
to highlight only variants with GnomAD
allele frequency of less than 0.05.
Deselecting the Highlight option would
display only those variants that match
the filter.
Geneticist Assistant can also be
integrated with NextGENe to provide
a complete, seamless pipeline from
alignment and variant calling to variant
interpretation.
Compatible
Databases
Functional Prediction Information:
SIFT, PolyPhen2, LRT, Mutation Taster,
FATHMM, CADD & Mutation Assessor
Disease Association:
ClinVar, OMIM & COSMIC
Conservation Scores:
PhyloP, GERP++, phastCons & SiPhy
Population Frequencies:
1000 Genomes, GnomAD, ExAC, and Exome
Variant Server
Additionally, information from proprietary
databases such as Alamut and LOVD
is easily accessible through embedded
links. Information from other publicly
available databases is also easily
imported into the workbench.
Unique tools, including Quality Metrics
Assistant, in conjunction with NextGENe
software can form a completely automated
informatics pipeline.
Webinars
Getting Started (View)
(view
on  )
The benefits of Geneticist Assistant
(View)
(view
on )
Submitting and Reviewing Data (View)
(view
on )
|
