Sample Sex

Use the --sample-sex command line option to control the sex karyotype input used in downstream components, such as variant callers. If a sample sex karyotype input is not specified using the command line, the sex karyotype is automatically determined. The sex karyotype input is converted to a reference sex karyotype for use in variant calling. Other components might support sex karyotype input. Refer to the corresponding section for the component you are using.

The --sample-sex option supports the following values. Values are not case-sensitive.

•

none—No sex karyotype input. Components use a default reference sex karyotype.

•

auto—The sex karyotype is estimated by the Ploidy Estimator. If using CNV calling, sex karyotype is determined using a separate sex estimation module. If DRAGEN cannot estimate the sex karyotype, then components do not have a sex karyotype input. This behavior is then the same as none. auto is the default value.

•

female—Sex karyotype input is XX.

•

male—Sex karyotype input is XY.

The following example command lines use --sample-sex to specify the sex karyotype.

If the value is none, female, or male, the Ploidy Estimator could still run and produce output, but variant callers will not use any estimated sex karyotype that is different than the sex karyotype specified via the command-line.

The sex karyotype input is converted to the reference sex karyotype for the different components as follows. See the relevant component section for more information on how --sample-sex is used.

Sex Karyotype Input	CNV Caller	ExpansionHunter	Ploidy Caller	Small Variant Caller	SV Caller
XX	XX	XX	XX	XX	XXYY
XY	XY	XY	XY	XY	XXYY
XXY	XY	XX	XY	XXYY	XXYY
XYY	XY	XY	XY	XXYY	XXYY
X0	XX	XY	XX	XXYY	XXYY
XXXY	XY	XX	XY	XXYY	XXYY
XXX	XX	XX	XX	XXYY	XXYY
None	XX	XX	XX	XXYY	XXYY