Ploidy Estimator

The Ploidy Estimator runs by default. The Ploidy Estimator uses reads from the mapper/aligner to calculate the sequencing depth of coverage for each autosome and allosome in the human genome. The sex karyotype of the sample is then estimated using the ratios of the median sex chromosome coverages to the median autosomal coverage. The sex karyotype is estimated based on the range the ratios fall in. If the ratios are outside all expected ranges, then the Ploidy Estimator does not determine a sex karyotype.

Sex Karyotype	X Ratio Min	X Ratio Max	Y Ratio Min	Y Ratio Max
XX	0.75	1.25	0.00	0.25
XY	0.25	0.75	0.25	0.75
XXY	0.75	1.25	0.25	0.75
XYY	0.25	0.75	0.75	1.25
X0	0.25	0.75	0.00	0.25
XXXY	1.25	1.75	0.25	0.75
XXX	1.25	1.75	0.00	0.25

Ploidy estimation can fail if the type of input sequencing data cannot be determined or if there is not sufficient sequencing coverage in the autosomes. When ploidy estimation fails the estimated median coverage values will be zero.

When both tumor and matched normal reads are provided as input, the Ploidy Estimator only estimates sequencing coverage and sex karyotype for the matched normal sample and ignores the tumor reads. If only tumor reads are provided as input, the Ploidy Estimator estimates sequencing coverage and sex karyotype for the tumor sample.