Sex Classifier algorithm (SAM/BAM)

1) Calculate the per-contig Depth as described in Coverage and Depth.

2) Calculate X_Depth / Y_Depth and chr1_Depth / X_Depth.

3) Decision matrix:

Assigned Sex

1 / X

X / Y

Male

> 1.75 (single-X)

< 9 (Has Y)

Female

< 1.1 (double-X)

> 5 (Not enough Y for Male)

Female

< 1.3 (not quite double-X)

> 9 (No Y)

Male-XXY

< 1.1 (double-X)

∈ (1.8,5) (XXY)

Male-XXY or XY/XXY mosaic

∈ (1.1, 1.3) (not quite double-X)

∈ (1.8,5) (XXY)

Male-XXY or XXYY

< 1.1 (double-X)

< 1.8 (Has Y, possibly similar ratio Y to X)

Unassigned

All other combinations

Definitions:
Depth is defined here Coverage and Depth.

Chromosome X is the contig named “X”, “chrX” or “ChrX”, and similarly for Y and chr1.