The NextGENe 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 dbNSFP, dbSNP, gnomAD 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, or similarity or differences between the samples
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.
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 2: The Variant Comparison tool comparing 3 samples. A report table and alignment view for each sample is displayed.
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