Sample gender

Several analysis workflows in Ion Reporter™ Software, especially copy number variation detection and Ion AmpliSeq™ IDP trio, are limited when the sample gender is unknown, and they return unexpected results when the gender is incorrectly specified.

For example, in the Ion AmpliSeq™ IDP trio analysis workflow, when the gender of the proband is not known, variants cannot be assigned in the categories HasMaleMaternalX and HasUnknownX.

If a sample with no gender is transferred from Torrent Suite™ Software to Ion Reporter™ Software, you can go to the Define Samples step in Ion Reporter™ Software and edit the sample to specify the gender attribute.

Note:

  • You cannot edit samples that have been launched in an Ion Reporter™ Software analysis. Instead, define new samples from the BAM or VCF data files, and add the correct gender metadata to the new samples.

  • If the gender of the sample is not specified or is specified as "Unknown", the Integrative Genomics Viewer uses female as the gender.

Related Topics
Parent topic: Automatically transfer Torrent Suite™ Software output to Ion Reporter™ Software