The gender attribute is a unique sample attribute that is used in various ways. The gender attribute is used by some analysis workflows in Ion Reporter™ Software, including the Ion AmpliSeq™ Exome trio and Ion AmpliSeq™ IDP trio analysis workflows
Several analysis workflows, such as the Ion AmpliSeq™ IDP trio analysis workflows, are limited when the sample gender is Unknown. These analysis workflows return unexpected results when 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.
Gender can be supplied by the Planned Run in Torrent Suite™ Software. You can also add or change the gender attribute when you import a sample, or edit a sample in Ion Reporter™ Software. For example, if a sample that was transferred from Torrent Suite™ Software to Ion Reporter™ Software does not include the gender attribute or includes an attribute value that is not correct, you can edit the sample to add the gender attribute, or change its value.
To edit the gender attribute, first define new samples from the BAM or VCF data files. Then you can add the correct gender information to the new sample. For more information, see Define samples with one or more BAM files and Define a single VCF file as a sample.
Note: Called Gender is another sample attribute that is calculated for some types of analyses and shown in the analysis results. The Called Gender sample attribute cannot be edited or defined manually. The software calculates Called Gender using an algorithm based on the analysis of sex chromosome data.