Ploidy Support

The small variant caller currently only supports either ploidy 1 or 2 on all contigs within the reference except for the mitochondrial contig, which uses a continuous allele frequency approach (see Mitochondrial Calling). The selection of ploidy 1 or 2 for all other contigs is determined as follows.

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If --sample-sex is not specified on the command line, the Ploidy Estimator determines the sex. If the Ploidy Estimator cannot determine the sex karyotype or detects sex chromosome aneuploidy, all contigs are processed with ploidy 2.

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If --sample-sex is specified on the command line, contigs are processed as follows.

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For female samples, DRAGEN processes all contigs with ploidy 2, and marks variant calls on chrY with a filter PloidyConflict.

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For male samples, DRAGEN processes all contigs with ploidy 2, except for the sex chromosomes. DRAGEN processes chrX with ploidy 1, except in the PAR regions, where it is processed with ploidy 2. chrY is processed with ploidy 1 throughout.

DRAGEN detects sex chromosomes by the naming convention, either X/Y or chrX/chrY. No other naming convention is supported.

 

--sample-sex	Ploidy Estimation	Sample Sex in Small VC
male	Not relevant	Male
female	Not relevant	Female
Not specified	XY	Male
Not specified	XX	Female
Not specified	Everything else	None