Infer copy number segments from the given coverage table. Segmentation runs independently on each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
- Segmented log2 ratios (.cns) output file contains those columns
- chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
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). |
Segmented log2 ratios (.cns)
Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
| chromosome | start, end: Genomic coordinates of the segment |
| gene | Gene(s) overlapping the segment. |
| log2 | Mean log2 ratio of the segment. |
| probes | Mean log2 ratio of the segment. |
| depth | Average read depth. |
| weight | Reliability weight. |
| p_value | Statistical confidence (lower = more significant). |