Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y. The output is a table of the sample name (derived from the filename), inferred sex (string “Female” or “Male”), and log2 ratio value of chromosomes X and Y.
Bin-level log2 ratios (.cnr)
Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
| chromosome | Genomic chromosome (e.g., chr1, chrX) |
| start | Start position of the bin. |
| end | End position of the bin. |
| gene | Gene name(s) overlapping the bin (if applicable). |
| log2 | Normalized log2 ratio (sample coverage / reference coverage). |
| depth | Average read depth in the bin. |
| weight | Reliability weight of the bin (higher = more reliable). |