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Annotation Tracks

The Track Manager tool in NextGENe allows for import of variant annotation from external databases that can be automatically queried for use in both the mutation report (figure 1) and the variant comparison report. Tracks such as dbSNP, COSMIC, 1000 genomes, dbNSFP, and NHLBI GO Exome Sequencing Project (ESP) can be added to your projects, as well as your own custom database. Once a track is imported for a given genome build, it can be automatically queried for every new project run against that genome or it can be queried manually in the NextGENe Viewer.

 

 

Figure 1: The NextGENe Mutation Report with annotation from multiple tracks.

 

There are four databases with specialized support. More information on some of these can be found in the ‘References' dialog of the NextGENe ‘Help' menu.

• dbNSFP (Database of Non-Synonymous Functional Prediction) - Functional Prediction, Conservation, and (when available) population frequency information is available for all non-synonymous SNPs

  • dbscSNV – in attached database with dbNSFP – functional annotations and ensemble

    predictions for splice site substitutions

  • COSMIC (Catalog of Somatic Mutations in Cancer)

  • dbSNP/ClinVar

There is also a Custom Variant Track import option that can be used to import other databases not specifically listed above.

 

 

Querying Tracks in the Viewer

The "Query Reference Tracks" dialog can be used to import or update track information in an alignment project.

The available tracks for the applicable genome build for the project are listed (figure 2). Each track can be either selected so that it can be used in the reports for the project or can be deselected.

 

Figure 2: The "Query Reference Tracks" dialog.

 

 

Filtering using Tracks

 

For any track that is selected for a project, there are both display and filtering options available in the Variation Tracks Settings dialog (figure 3). You can select any track on the left side to define the any filtering settings for track, and/or to click "Report Display" to choose which columns for the track to include in the report.

 

Figure 3: The Variation Tracks Settings dialog, dbNSFP track filter options shown.

 

 

 

For More Information Review or Download Application notes:
Add Annotation Tracks from External Databases to NextGENe
Finding Causative Mutation Candidates from NGS Sequencing
Reducing error of NGS Sequencing data with NextGENe Condensation™ Tool
Alignment of PGM PE reads with NextGENe software
Processing Paired End Sequencing Data from the Ion PGM™ Sequencer with NextGENe® Software
Processing Ion PGM™ Sequencing Data with NextGENe Software
Processing CFTR Amplicon Data from the Ion PGM™ using NextGENe® Software
Processing Ion AmpliSeq™ Cancer Panel Data using NextGENe® Software
Amplicon Sequence Analysis of Sanger Sequences and Ion PGM data
NextGENe Illumina SNP_Indel_Detection
NextGENe SNP_ Indel_Discovery_SOLID
SNP_INDEL_detection_Roche454
Structural Variant Analysis
NextGENe software Variant Comparison Tool
Mutation Confidence Scoring with NextGENe software
NextGENe SNP & Indel Viewer
Deep Sequence Analysis with NextGENe software
Whole Genome Alignment with NextGENe software
Sequence Capture Analysis with NextGENe software
Paired end read merging with NextGENe software
Sequence Analysis Using Barcode/Index Tags of Pooled Samples with NextGENe Software
Using NextGENe software's Pipeline Automation Tool
Plugin for Torrent Browser automation
Demultiplexing Illumina® MiSeq™ Data

 

Pricing & Trial Version:
Request 30-day trial/Price Quote

 

Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes

 

Track Manager Manual
Use the Reference & Track Manager tool to import and manage preloaded references and data from any public or proprietary variant database.
Download the manual

 

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