SoftGenetics - Software PowerTools for Genetic Analysis
 
       

 

Trio and Multi-Sample Variant Comparison

NextGENe's Variant Comparison Tool can be used to compare variants detected across samples, including trio analysis, tumor-normal pairs and other comparisons. This is a valuable tool to quickly sort through thousands of mutation calls in order to find a few dozen (or even fewer) candidate mutations that can be confirmed with Sanger sequencing and assessed for their phenotypic impact. Information from imported tracks, such as COSMIC, dbNSFP, dbSNP and any custom tracks, can be displayed in the comparison tool and can also be used for filtering the variants included in the report.

 

There are multiple options available for creating the comparison:
• Based on sample relationships, phenotypes and the applicable inheritance pattern
• Based on specified mutation types in each sample
• Show shared variants
• Show different variants

 

 

Figure 1: Specify relationships and phenotypes for each sample to compare variants based on an inheritance pattern. The applicable inheritance pattern can be selected in the next dialog.

 

 

Figure 2: A template for the applicable inheritance pattern can be selected. Other comparison options include showing only shared or only different variants across the samples, or showing variants that match defined mutation types for each sample.

The resulting comparison view includes a report table as well as visualization for each sample side by side. The table and visualization are linked - double-clicking on any variant in the report directly loads the visualization for that position in all samples.

 

 

Figure 3: The Variant Comparison tool comparing 3 samples. A report table and alignment view for each sample is displayed.

For More Information Review or Download Application notes:
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

 

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SoftGenetics - Software PowerTools for Genetic Analysis
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