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

The output field or fields for linearized coordinates.

channel

Get the genome assembly from the scale of the channel.

Default: "x"

chrom Required

The chromosome/contig field

offset

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

The field or fields that contain intra-chromosomal positions

Example

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