PlinkLDTabixAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the variants plugin. View source.

Example usage#

{
  type: 'LDTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'PlinkLDTabixAdapter',
    uri: 'https://example.com/study.sorted.ld.gz',
  },
}

study.sorted.ld.gz infers PlinkLDTabixAdapter and LDTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/study.sorted.ld.gz',
  assemblyNames: ['hg38'],
}

See the Config slots section below for all available configuration fields.

Adapter for reading pre-computed LD data from a PLINK LD table (tabix-indexed), either PLINK 2.0's .vcor or PLINK 1.9's .ld.

The input file should be bgzipped and tabix-indexed:

plink2 --bfile study --r2-unphased --out study
# plink2 writes tabs and comments its own header, so sort-bed takes the table
# as it is; sort-bed is `sort -k1,1 -k2,2n` under LC_ALL=C with the `#` line
# kept on top
jbrowse sort-bed < study.vcor | bgzip > study.sorted.ld.gz
tabix -s 1 -b 2 -e 2 study.sorted.ld.gz

PLINK 1.9 writes the same table space-padded with a bare header, so there it needs a retab first:

plink --bfile study --r2 --out study
awk 'NR == 1 {$1 = "#"$1} {$1 = $1}1' OFS='\t' study.ld |
  jbrowse sort-bed | bgzip > study.sorted.ld.gz

Comment the header with # rather than counting it with tabix -S 1. Both keep it out of the data, but only the commented form is what tabix -H prints and what readers ask for first, so a -S 1 header is easy to miss — and missing it means missing the D' column, which is what makes D' available instead of only r². (Not -c C: that makes C the meta character, so every chr1-style data row would read as a comment.) A file already indexed with -S 1 still loads.

Expected columns, either spelling: CHR_A BP_A SNP_A CHR_B BP_B SNP_B R2, or plink2's CHROM_A POS_A ID_A CHROM_B POS_B ID_B PHASED_R2 (UNPHASED_R2 for the other statistic). Optional columns: DP / ABS_DPRIME / DPRIME (D'), MAF_A MAF_B / NONMAJ_FREQ_A NONMAJ_FREQ_B. A signed DPRIME is read as its magnitude, which is all a pre-computed cell can be drawn as.

study.vcor before bgzipping, plink2 adding cols= for anything past r²:

#CHROM_A	POS_A	ID_A	CHROM_B	POS_B	ID_B	UNPHASED_R2
1	729679	rs4970383	1	752566	rs3131972	0.0925926
1	729679	rs4970383	1	754182	rs3131969	0.157316

Used by the variant LD display (triangular r² heatmap) and by GWAS Manhattan LD coloring (LocusZoom-style r² to an index SNP). See either guide for generating the table. --r2-phased is the statistic the LD display computes from genotypes, so it is the one whose cells compare with a live triangle.

Related links#

• Track: LDTrack
• Display: LDTrackDisplay
• Guide: GWAS track
• Guide: LD across an inversion (mosquitoes)
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "PlinkLDTabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi in place of writing a location slot out. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.