> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/annotation/data-sources/decipher.md). # DECIPHER ### Overview [DECIPHER](https://www.deciphergenomics.org/) (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. {% hint style="info" %} **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) {% endhint %} #### TSV Extraction ```scss #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 #### JSON output ```json "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 | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/annotation/data-sources/decipher.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.