CpG Island

Overview

This supplementary data is one of the supplementary data that will only be used for annotating methylation gVCF file. In general, this supplementary data define genoimic region interval that indicates CpG island. The suppplementary data is available for both GRCh37 and GRCh38. Both data is obtained from publicly available source from UCSC FTP.

File URL for GRCh37

File URL for GRCh38

The file schema is explained in this link

Parsing

From those TSV file, we read every entry and store all info so that we can produce those data in the output.

Output

An example of methylation annotation from CpG Island region is below

{
  "chromosome": "21",
  "begin": 20997105,
  "end": 20998245,
  "regionId": "CpG: 89",
  "biotype": "cpgIsland",
  "bin": 745,
  "length": 1140,
  "cpgNum": 89,
  "gcNum": 674,
  "percentageCpg": 15.6,
  "percentageGc": 59.1,
  "observedToExpectedRatio": 0.89,
  "samples": [
    {
      "sampleId": "mate_len_200bp_100X",
      "averageCpGMethylation": 0.5085069662921352,
      "totalCpGCoverage": 5413,
      "totalCpGPosition": 44.5
    }
  ]
}

The output includes the biotype cpgIsland and contains additional fields derived from the supplementary data.

The following table describes these extra fields:

Field	Description
bin	Indexing bin used for efficient spatial querying.
length	Total length of the CpG island region.
cpgNum	Number of CpG dinucleotides within the island.
gcNum	Number of G and C nucleotides within the island.
percentageCpG	Percentage of CpG dinucleotides in the region.
percentageGc	Percentage of GC content in the region.
observedToExpectedRatio	The ratio of observed to expected CpG counts.
regionId	Corresponds to the name column from the original UCSC TSV file.