Parameter Settings defaults

The variantCaller plugin parameter settings change according to your Variant Caller configuration radio button selection. Data from Ion PGM™ and Ion Proton™ Sequencers require different default settings. Select settings that are appropriate to both your sequencing instrument and your experiment:

Germ-Line - Low Stringency Optimized for high frequency variants and minimal false negative calls.
Somatic - Low Stringency Optimized for low frequency variant detection with minimal false negative calls.
Germ-Line - TargetSeq Low Stringency Optimized for high frequency variants and minimal false negative calls. (Ion Proton™ data only)
Custom Settings that you customize. (You cannot select this radio button. This button is enabled if you change a parameter value.)

Ion AmpliSeq™ and TargetSeq™ experiments

Note:

The following setings are optimized for IonTargetSeq experiments:

Germ Line - Proton TargetSeq -Low Stringency

For Ion AmpliSeq™ experiments, when you import your template from AmpliSeq.com, your template and run plans are already pre-configured with parameters that are optimized for your panel.