Sample gender

Whenever the gender of a sample is known, enter the gender in the plan (the gender column is not shown in the example images). Several workflows, especially copy number variation detection and Genetic Disease Screening (GDS), are limited when gender is not known and also return unexpected results when gender is incorrectly specified for a sample.

For example, with the (GDS) workflow, when the gender of the proband is not known, variants cannot be assigned the categories HasMaleMaternalX and HasUnknownX.

If you transfer a research sample without specifying the gender, follow this step as a workaround: after the files are transferred, go to the Sample > Sample Management screen in Ion Reporter™ Software and edit the GDS sample to specify the gender attribute.

Note:

You cannot edit samples that have been launched in an analysis. Instead, define new samples from the raw data files, and add the correct gender metadata to the new samples.

Note about sample gender for Ion Reporter™ Software users:

IGV assumes that a sample's gender is female, if the sample's gender is not specified or specified as "Unknown".