DECIPHER

Overview

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants.

DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient. The patient's variant is displayed in the context of both normal variation and pathogenic variation reported at that locus thereby facilitating interpretation.

Publication

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth, H.V. et al., 2009. Am.J.Hum.Genet 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)

TSV Extraction

#population_cnv_id  chr start   end deletion_observations   deletion_frequency  deletion_standard_error duplication_observations    duplication_frequency   duplication_standard_error  observations    frequency   standard_error  type    sample_size study
1   1   10529   177368  0   0   1   3   0.075   0.555277708 3   0.075   0.555277708 1   40  42M calls
2   1   13516   91073   0   0   1   27  0.675   0.109713431 27  0.675   0.109713431 1   40  42M calls
3   1   18888   35451   0   0   1   2   0.002366864 0.706269473 2   0.002366864 0.706269473 1   845 DDD

Parsing

We parse the DECIPHER tsv file and extract the following columns:

• chr
• start
• end
• deletion_observations
• deletion_frequency
• duplication_observations
• duplication_frequency
• sample_size

Download URL

https://www.deciphergenomics.org/files/downloads/population_cnv_grch38.txt.gz https://www.deciphergenomics.org/files/downloads/population_cnv_grch37.txt.gz

JSON output

"decipher":[
  {
    "chromosome":"1",
    "begin":13516,
    "end":91073,
    "numDeletions":27,
    "deletionFrequency":0.675,
    "numDuplications":27,
    "duplicationFrequency":0.675,
    "sampleSize":40,
    "reciprocalOverlap": 0.27555,
    "annotationOverlap": 0.5901
  }
],

Field	Type	Notes
chromosome	int	Ensembl-style chromosome names
begin	int	1-based position
end	int	1-based position
numDeletions	int	# of observed deletions
deletionFrequency	float	deletion frequency
numDuplications	int	# of observed duplications
duplicationFrequency	float	duplication frequency
sampleSize	int	total # of samples
reciprocalOverlap	float	Range: 0 - 1. E.g. 0.57 would indicate a 57% reciprocal overlap
annotationOverlap	float	Range: 0 - 1. E.g. 0.57 would indicate a 57% annotation overlap