copy_number_regions
Read-only
Place an Affymetrix copy-number sample's own calls in ClinGen's curated regions: for each region, which gains, losses or stretches of homozygosity fall in it, at what reciprocal overlap, and how much of the region they cover between them. Regions come from ClinGen's dosage-sensitivity curation, cached with its retrieval date — a loss is reported against the region's haploinsufficiency score and a gain against its triplosensitivity score, and no score is claimed for LOH or mosaic events, which change no copy number. NO THRESHOLD IS APPLIED: every overlap is reported with its numbers and which calls are worth reporting is a laboratory's judgement. Regions ClinGen has not placed on this build are listed separately and are NOT reported as clean.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file | No | which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one. | |
| build | No | which assembly's curated region list to place the calls on. Unset is the build THIS FILE states about itself, and the node refuses rather than guessing when it states none — a region is a pair of coordinates, and placing a call on the wrong assembly moves every boundary by hundreds of kilobases with nothing to show it. Values: hg19 (hg19 / GRCh37), hg38 (hg38 / GRCh38). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| regions | No | a BED region file in this project, by name, to check against INSTEAD of ClinGen's curated list — the laboratory's own panel, which is what ChAS calls the CytoRegion file. Unset is ClinGen. A BED line states no dosage score, so with this set every hit comes back with dosage null: the list says where to look and claims nothing about what a change there means. If the file states an assembly on its track line (`track ... db=hg19`) and it is not the build being read, the node refuses rather than moving every boundary by hundreds of kilobases. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| data_set | No | which data set to scan, by name. Unset is the file's FIRST, which is what the panel opens on. | |
| min_bases | No | ignore any call spanning fewer bases than this. Default 0, for the same reason as min_markers. Note a single-marker call spans 0 bases. | |
| min_markers | No | ignore any call shorter than this many markers. The default counts everything the file called, because a reporting floor belongs to the laboratory and not to this tool — and it is the same floor copy_number_findings applies, so both doors place the same calls. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| regions | Yes | one entry per curated region containing at least one call: id (the ISCA identifier a report cites), name, cytoband, chrom, start, end (0-based half-open), covered (fraction of the region the calls cover between them, each base counted once, so it never exceeds 1), counts by finding kind, and hits — each with the finding itself, overlapBases, reciprocalOverlap (the SMALLER of the two containment fractions, so a focal call inside a whole-arm region scores low rather than 100%), regionCovered, and dosage/dosageAxis: ClinGen's score and description for the axis that speaks to that call's direction, or null for LOH and mosaic events, which change no copy number | |
| summary | Yes | how many curated regions contain a call, out of how many were checked, on which build | |
| unplaced | Yes | curated regions ClinGen has NOT placed on this build — it states their location as 'tbd'. They carry id, name, cytoband and their dosage scores but no coordinates, so nothing could be checked against them. They are NOT clean: they are unchecked. Empty on hg19, which places all of them | |
| provenance | Yes | which region list answered: its authority, source URL, the curation date the file states, the assembly, and how many regions were placed and unplaced. A cached copy of an authority's table is only interpretable with its version beside it |