Getting Started with GeneMarkerHTS
The GeneMarkerHTS Main Window
Title bar
Main menu
Application Settings icon
Project options
About button
Help button
Status bar
GeneMarkerHTS Project Setup and Management
New Project Dialog Box Settings
Folders and Paths
Motifs
Overview of using a motif
To create or edit a custom motif
Panel and Panel Options
Alignment Options: Optional Steps
Alignment Options: Filters/Clipping
Soft clipping based on quality scores
Amplicon Settings
Specifying amplicon regions
To load an amplicon BED file
To manually add amplicon regions
PHI Settings
Masking personal health information (PHI) for a subject
Working with a GeneMarkerHTS Project
New GeneMarkerHTS project caveats
To add a new GeneMarkerHTS project
To work with an existing GeneMarkerHTS project
GeneMarkerHTS Project Output Files
GeneMarkerHTS Viewers and Reports
Mito Alignment Viewer Overview and Layout
Mito Alignment viewer title bar
Mito Alignment viewer main menu
View on EMPOP Database dialog box
Global Viewer pane
To save the Global Viewer pane display as an image
Pane displays
Reference pane
Consensus pane
Motifs and Amplicons pane
Pile-Up pane
Variants table
Status Bar
Mito Alignment Viewer Navigation and Options
Mito Alignment viewer navigation
Mito Alignment viewer variant-specific viewing and editing options
To add a variant at a given position
To delete a variant at a given position
To save/load reports for an mtDNA project
To save a report for an mtDNA project
To load a report for an mtDNA project
Mito Alignment Viewer Filter Settings
To specify the variant call settings for an mtDNA project
Allele Score Difference
Allele Balance Ratio
To set the reference region settings for an mtDNA project
Mito Alignment Table Settings
To specify the table settings for an mtDNA project
Mito Alignment Viewer Reports
Coverage report
To change the Coverage Report display
To save the low coverage regions as a text file
Template Length report
Read Length report
STR Analysis Viewer Overview and Layout
STR Analysis viewer title bar
STR Analysis viewer main menu
STR Analysis viewer reports
Viewer Options menu
Histogram Viewer pane
Histogram context menu
Histogram Settings dialog box
STR Results Table pane
To work with the STR Results Table pane configuration
To include filtered rows in the STR Results Table pane
To manually edit the STR Results Table pane configuration
To edit the STR Results Table pane configuration by loading a file
To work with user calls and comments in the STR Results Table pane
To enter or edit a custom user call
To enter comments for a result in the STR Results Table pane
To clear a custom user call
STR Analysis Viewer STR and STR Stutter Filter Settings
Filter Settings dialog box, STR Filter Tab
To edit the STR Filter tab configuration
To specify the STR filter settings for an STR analysis project
To edit the STR filter settings
To load an STR/STR Stutter filter settings file
To import an STR Filter tab-specific filter settings file
To finish specifying the settings for an STR analysis project (STR tab)
To save the STR filter settings before applying them
To export the STR filter settings before applying them
Filter Settings dialog box, STR Stutter Tab
To edit the STR Stutter tab configuration
To specify the STR Stutter filter settings for an STR analysis project
To edit the STR Stutter filter settings
To load an STR/STR Stutter filter settings file
To import an STR Stutter tab-specific filter settings file
To finish specifying the settings for an STR analysis project (STR Stutter tab)
To save the STR Stutter filter settings before applying them
To export the STR Stutter filter settings before applying them
Comparison Viewer
Comparison viewer main menu
Sample to Sample Comparison pane
Variant Comparison pane
GeneMarkerHTS Application Settings
GeneMarkerHTS Application Settings Dialog Box Layout
Configuring GeneMarkerHTS Project Directory Settings
To configure GeneMarkerHTS project directory settings
Configuring GeneMarkerHTS License Settings
To set a Trial license
Configuring GeneMarkerHTS Visuals Settings
To edit the Visuals application settings
To edit the bracket sequence settings
To edit the background and highlighting colors in the Pile-up pane display
To edit the visibility and default nucleotide colors for the Pile-up pane display
To edit the Global Viewer pane colors
To edit the Variants table (Report Table) Category colors
To edit the Comparison viewer variant highlighting colors
To edit the STR Analysis viewer highlighting colors
Glossary