Sample Sex

Use the --sample-sex option to specify the sample sex on the command line. The information is passed to all callers. The CNV caller contains a separate sex inference feature, but the specified --sample-sex takes precedence over the inferred sex. The following example specifies sample sex using the --sample-sex option:

--sample-sex MALE

--sample-sex FEMALE

If --sample-sex is not specified on the command line, the Ploidy Estimator runs by default to determine the sex.