Linearize Genomic Coordinate

The linearizeGenomicCoordinate transform maps the (chromosome, position) pairs into a linear coordinate space using the chromosome sizes of the current genome assembly.

Parameters

as Required

Type: string | string[]

The output field or fields for linearized coordinates.

channel

Type: string

Get the genome assembly from the scale of the channel.

Default: "x"

chrom Required

Type: string (field name)

The chromosome/contig field

offset

Type: number | number[]

An offset or offsets that allow for adjusting the numbering base. The offset is subtracted from the positions.

GenomeSpy uses internally zero-based indexing with half-open intervals. UCSC-based formats (BED, etc.) generally use this scheme. However, for example, VCF files use one-based indexing and must be adjusted by setting the offset to 1.

Default: 0

pos Required

Type: string (field name) | string (field name)[]

The field or fields that contain intra-chromosomal positions

Example

{
  "type": "linearizeGenomicCoordinate",
  "chrom": "chrom",
  "pos": "start",
  "as": "_start"
}