GWAS Track

The GWAS track (type = 'gwas') is used for visualizing genome wide association data as a "manhattan" style plot

File formats#

GWAS tracks can be loaded from either bed or files.

bed#

5 columns (chromosome, start, end, name, value). Additional columns are ignored. Note bed format uses UCSC "0-based" positions, so the first position in the chromosome has start=0, end=1.

gwas#

This is a flexible tab-delimited format. Any number of columns are supported but must include chromosome, position (1- based), and value (p-value or probability). A column header is required. Position of the required columns can be specified in the file column header, as described below, or in the track configuration (see example). Remaining columns are used for the popup text display.

To specify column positions for the required fields include the following case-insensitive column headers in the header line.

• CHR: chromosome (aliases chr, chromosome)
• BP: nucleotide location (aliases bp, pos, position)
• SNP: SNP identifier (aliases snp, rs, rsid, rsnum, id, marker, markername)
• P: p-value for the association (aliases p, pval, p-value, pvalue, p.value)

Configuration Options#

Property	Description	Default
min	Sets the minimum value for the data (y-axis) scale.	0
max	Sets the maximum value for the data (y-axis) scale.	25 for p-value (-log10(pvalue)), 1 for posterior probability
format	File format, either "bed" or "gwas"
posteriorProbability	If true values are interpreted as probabilities with a range 0-1. By default values are treated as p-values and plotted as -log10(P-value).	false
dotSize	Diameter of dots in pixels	3
columns	For gwas format only. Declaration of column number for chromosome, position, and value. Optional, if specified all must be provided. See example below.	{chromosome: 2, position: 3, value: 4}
colorTable	Object mapping chromosome names -> colors. If supplied all chromosomes in data should be included. See below for the default color table	See below

Example#

{
   type: "gwas",
   format: "gwas",
   name: "GWAS sample",
   url: "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz",
   indexed: false,
   columns: {
      chromosome: 12,
      position: 13,
      value: 28
   }
}

Default color table#

{
    "X": "rgb(204, 153, 0)",
    "Y": "rgb(153, 204, 0)",
    "Un": "darkGray)",
    "1": "rgb(80, 80, 255)",
    "2": "rgb(206, 61, 50)",
    "2a": "rgb(210, 65, 55)",
    "2b": "rgb(215, 70, 60)",
    "3": "rgb(116, 155, 88)",
    "4": "rgb(240, 230, 133)",
    "5": "rgb(70, 105, 131)",
    "6": "rgb(186, 99, 56)",
    "7": "rgb(93, 177, 221)",
    "8": "rgb(128, 34, 104)",
    "9": "rgb(107, 215, 107)",
    "10": "rgb(213, 149, 167)",
    "11": "rgb(146, 72, 34)",
    "12": "rgb(131, 123, 141)",
    "13": "rgb(199, 81, 39)",
    "14": "rgb(213, 143, 92)",
    "15": "rgb(122, 101, 165)",
    "16": "rgb(228, 175, 105)",
    "17": "rgb(59, 27, 83)",
    "18": "rgb(205, 222, 183)",
    "19": "rgb(97, 42, 121)",
    "20": "rgb(174, 31, 99)",
    "21": "rgb(231, 199, 111)",
    "22": "rgb(90, 101, 94)",
    "23": "rgb(204, 153, 0)",
    "24": "rgb(153, 204, 0)",
    "25": "rgb(51, 204, 0)",
    "26": "rgb(0, 204, 51)",
    "27": "rgb(0, 204, 153)",
    "28": "rgb(0, 153, 204)",
    "29": "rgb(10, 71, 255)",
    "30": "rgb(71, 117, 255)",
    "31": "rgb(255, 194, 10)",
    "32": "rgb(255, 209, 71)",
    "33": "rgb(153, 0, 51)",
    "34": "rgb(153, 26, 0)",
    "35": "rgb(153, 102, 0)",
    "36": "rgb(128, 153, 0)",
    "37": "rgb(51, 153, 0)",
    "38": "rgb(0, 153, 26)",
    "39": "rgb(0, 153, 102)",
    "40": "rgb(0, 128, 153)",
    "41": "rgb(0, 51, 153)",
    "42": "rgb(26, 0, 153)",
    "43": "rgb(102, 0, 153)",
    "44": "rgb(153, 0, 128)",
    "45": "rgb(214, 0, 71)",
    "46": "rgb(255, 20, 99)",
    "47": "rgb(0, 214, 143)",
    "48": "rgb(20, 255, 177)"
}