Ploidy Estimator Reference Sex Karyotype

The estimated sex karyotype (if determined), is made available to downstream components (eg variant callers). For components that support using the estimated sex karyotype, refer to the corresponding section for more information. To overwrite the sex karyotype used by downstream components, use the --sample-sex command line option. If the value specified is male, then the sex karyotype is XY. If the value specified is female, then the sex karyotype is XX. The sex karyotype, whether provided via the command line or estimated, is converted to a reference sex karyotype for use as a baseline in variant calling.

The following table provides a summary of reference sex karyotypes and variant callers

Sex Karyotype	CNV Caller	ExpansionHunter	Ploidy Caller	Small Variant Caller	SV Caller
XX	XX	XX	XX	XXYY	XXYY
XY	XY	XY	XY	XY	XXYY
XXY	XY	XX	XY	XXYY	XXYY
XYY	XY	XX	XY	XXYY	XXYY
X0	XX	XX	XX	XXYY	XXYY
XXXY	XY	XX	XY	XXYY	XXYY
XXX	XX	XX	XX	XXYY	XXYY
Undetermined	XX	XX	XX	XXYY	XXYY

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The Copy Number Variant Caller utilizes its own estimation module that is largely consistent with the Ploidy Estimator. Any differences can be attributed to the read counting implementation.

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The Small Variant Caller marks chrY calls with the PloidyConflict filter when the sex karyotype is XX.

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The Structural Variant Caller always treats the sex chromosomes as diploid and does not take into account the sex karyotype.