NextGENe Online Help : NextGENe Viewer Reports and Tools : Sequence Alignment Project Mutation Report Settings : Mutation Report Settings dialog box : Filter tab, ROI sub-tab
Filter tab, ROI sub-tab
You can include or exclude variants from the Mutation report based on their locations in a Region of Interest (ROI) on the Filter tab, ROI sub-tab.
 
Setting
Description
Use ROIs in GenBank
Available only if the loaded project used a GenBank reference file. If you select this option, then you can also specify the number of bps before and after the ROIs to consider when calling mutations.
Use external ROIs
Available for any project. You can use ROIs that are defined in an external file. The external file can be a BED file, a comma-delimited text file that specifies position or gene name, or a VCF file. See External file types.
Tip: You can also click File Types to open a File Types dialog box that details the external files and their formats.
Include Negative Positions within ROI
Select this option to list every position in every ROI in the report, whether or not there is a variant at the position.
External file types
 
File Type
Description
BED file
A BED file is a tab-delimited text file. You can upload a BED file only if the reference sequence contains chromosome information, which means that the reference sequence must be either a preloaded reference that NextGENe supplies, or a GenBank reference file that contains chromosome information.
Text file
You can load a text file that is comma-delimited, semi-colon delimited, or tab-delimited. The file must contain one of the following lists:
• TXT Region Format - Specific reference locations (position number or a range of positions (start position number - end position number)).
• TXT Gene Format - A list of reference gene names.
VCF Format
You can upload a VCF file only if the reference sequence contains chromosome information, which means that the reference sequence must be either a preloaded reference that SoftGenetics supplies, or a GenBank reference file that contains chromosome information.
Note: See http://www.1000genomes.org for the conventions and extensions adopted by the 1000 Genomes Project for reporting variants in the most recent VCF format.