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 |