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Copy Number Variations (CNVs)

Information about the file/information format for somatic/germline CNVs.

Structure

Be aware that each of the following listings represent a tab-separated column field in the input SNV file. The column names in the header must be specified as followed:

'size'

A size description of the copy number variation. Currently an enumeration of:

  • chromosome
  • p-arm
  • q-arm
  • partial p-arm
  • partial q-arm
  • focal
  • non-focal
  • cluster

Example

size: q-arm

'type'

The copy number variation type. Currently an enumeration of:

  • del
  • dup
  • amp
  • loh
  • ins

Example

type: del

'copy_number'

The copy number of the variation.

Example

copy_number: 1

'gene'

HGNC formatted gene name.

Example

gene: tumor protein p53

'exons'

Information about the affected exons of a gene.

Example

exons: whole gene

'transcript'

Transcript reference identifier. Refseq or Ensembl.

Example

transcript: NM_001143990.1

'chr'

The chromosome location of the variant.

Example

chr: chr1

'start'

The genomic start position of the variant.

Example

start: 12500

'end'

The genomic end position of the variant.

Example

end: 13000

'effect'

The predicted or annotated effect of the variant. Currently an enumeration of:

Somatic CNVs:

  • activating
  • inactivating
  • function_changed
  • probably_activating
  • probably_inactivating
  • probably_function_change
  • ambigious
  • benign
  • NA

Germline CNVs (ACMG):

  • pathogenic
  • probably_pathogenic

Example

effect: activating