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CNVkit Genemetrics (version 0.9.12+galaxy0)

Bin-Level log2 Ratios/Coverages cnr file:

Use the output of the CNVkit fix

segmentation calls:

Otherwise inferred from file names

Min Number of covered probes:

Min Number of covered probes to report a gain/loss

threshold:

threshold

Assume inputs normalised to a male reference:

otherwise male samples would have -1 chrX

Drop very-low-coverage bins:

To avoid false-positive deletions in poor-quality tumor samples

Sample sex availabel:

Statistical settings

Statistical settings 0

Identify targeted genes with copy number gain or loss above or below a threshold. The first four columns of output table show each targeted gene’s name and its genomic coordinates (based on the first and last bins with that label in the original target BED file, and thus the .cnr file).

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).