Identify heterozygotes in chromatograms with secondary peak calling

Heterozygotes Plugin

This plugin Identifies heterozygotes in sequences with trace information by looking at the relative height of traces at peak positions.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a chromatogram sequence and choosing Annotate & Predict - Find Heterozygotes from the menu. Results can be saved as modifications to the sequence or as annotations.


2.0.0 (04 Aug 2019) – Download

– Fixed false positives

– Fixed false negatives

– Added new setting (“Peak Detection Height”) for finer grained tweaking of heterozygote detection

– Added new setting (“Minimum confidence to call heterozygote”) to prevent heterozygote detection in low quality regions

– Renamed “Minimum Confidence Score” to “Flag all positions with confidence below” to better reflect what that setting does.

– Added setting “Identify incorrect base calls when alternative peak height is” to detect clearly wrong base call

– Allow configuration of options when running from workflow

1.5.1 (06 Jul 2010) – Download

– Changes to sequence are undoable

– Appears in “Annotate and Predict” menu

– Fixed crash when trim region covers whole sequence

– Fixed crash when run on sequence with quality but no traces

1.2 (17 Jul 2008) – Download

– Now works on alignments and contigs

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