Please find below some useful links and publications to help you navigate and understand the data.
External links on this page can only be accessed from outside the RE
Research Environment Useful Links
| Link | URL |
|---|---|
| Research Environment | https://re.extge.co.uk/ovd/ |
| File Transfer Application | https://airlock-staging.extge.co.uk/ |
| Genomics England Service Desk | https://jiraservicedesk.extge.co.uk/servicedesk/customer/portals |
Technical Documentation
| Document | Version | Link |
|---|---|---|
Illumina Whole Genome Sequencing Services Guide | December 2015 | |
Illumina Cancer Analysis Services Guide | December 2015 | |
Rare Disease Results Guide | v5.0 | |
Cancer Genome Analysis Guide | v1.11 | |
PanelApp Handbook | v7 | |
International statistical classification of diseases and related health problems (ICD-10) | v10 | |
Exomiser (Improved exome prioritization of disease genes through cross-species phenotype comparison) | - | |
| Rare Disease Conditions Phenotypes and Clinical Tests (Clinical Data Models) | v1.9.0 |
Publications and other useful links
| Publication | URL |
|---|---|
| Improved exome prioritization of disease genes through cross-species phenotype comparison | https://www.ncbi.nlm.nih.gov/pubmed/24162188 |
| Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms | https://www.ncbi.nlm.nih.gov/pubmed/23736529 |
| Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs | https://www.ncbi.nlm.nih.gov/pubmed/22581179 |
| Strelka2: fast and accurate calling of germline and somatic variants | https://www.ncbi.nlm.nih.gov/pubmed/30013048 |
| Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications | https://www.ncbi.nlm.nih.gov/pubmed/26647377 |
| Canvas: versatile and scalable detection of copy number variants | https://www.ncbi.nlm.nih.gov/pubmed/27153601 |
| ExpansionHunter: Detection of long repeat expansions from PCR-free whole-genome sequence data | https://www.ncbi.nlm.nih.gov/pubmed/28887402 |
| Platypus: a tool designed for efficient and accurate variant-detection in high-throughput sequencing data | https://www.ncbi.nlm.nih.gov/pubmed/25017105 |
| Signatures of Mutational Processes in Human Cancer | https://cancer.sanger.ac.uk/cosmic/signatures |
| PONnoise50SNV: SNVs resulting from systematic mapping and calling artefacts |