Ploidy Caller Reference Sex Karyotype
In addition to detecting aneuploidy and chromosomal mosaicism in autosomes where the expected reference ploidy is two, the Ploidy Caller can also detect these variants in allosomes.
The reference sex karyotype used for making calls on the allosomes is determined from the sex karyotype of the sample either provided on the command line using --sample-sex or from the Ploidy Estimator. If the sex karyotype of the sample is not provided on the command line and not determined by the Ploidy Estimator, then the sex karyotype is assumed to be XX. Whenever the sex karyotype contains at least one Y chromosome, the reference sex karyotpye is XY. If the sex karyotype does not contain at least one Y chromosome, then the sex karyotype is XX.
The following table displays each of the possible sex karyotypes for a sample. If the Y chromosome reference ploidy is zero, then ploidy calling is not performed on the Y chromosome.
|
Sex Karyotype |
X Reference Ploidy |
Y Reference Ploidy |
|---|---|---|
|
XX |
2 |
0 |
|
XY |
1 |
1 |
|
XXY |
1 |
1 |
|
XYY |
1 |
1 |
|
X0 |
2 |
0 |
|
XXXY |
1 |
1 |
|
XXX |
2 |
0 |