Please find below some useful links and publications to help you navigate and understand the data.
Research Environment Useful Links
| Link | URL |
|---|---|
| Research Environment | https://re.extge.co.uk/ovd/ |
| Staging Environment | http://re-staging.extge.co.uk/ |
| 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 | v4.0 | |
Cancer Analysis Technical Information Document | 1.11 | |
PanelApp Handbook | v6.6 | |
International statistical classification of diseases and related health problems (ICD-10) | v10 | |
Exomiser (Improved exome prioritization of disease genes through cross-species phenotype comparison) | - |
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 |