{"id":21547942,"url":"https://github.com/illumina/platinumgenomes","last_synced_at":"2025-03-18T01:47:21.467Z","repository":{"id":56764786,"uuid":"101763913","full_name":"Illumina/PlatinumGenomes","owner":"Illumina","description":"The Platinum Genomes Truthset","archived":false,"fork":false,"pushed_at":"2017-11-08T19:25:45.000Z","size":9,"stargazers_count":85,"open_issues_count":8,"forks_count":9,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-01-24T09:27:42.450Z","etag":null,"topics":["indels","snvs","variant-analysis"],"latest_commit_sha":null,"homepage":"https://illumina.github.io/PlatinumGenomes","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Illumina.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-08-29T13:23:11.000Z","updated_at":"2024-11-14T22:54:15.000Z","dependencies_parsed_at":"2022-08-16T02:10:38.170Z","dependency_job_id":null,"html_url":"https://github.com/Illumina/PlatinumGenomes","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2FPlatinumGenomes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2FPlatinumGenomes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2FPlatinumGenomes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2FPlatinumGenomes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Illumina","download_url":"https://codeload.github.com/Illumina/PlatinumGenomes/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244141572,"owners_count":20404835,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["indels","snvs","variant-analysis"],"created_at":"2024-11-24T06:16:46.258Z","updated_at":"2025-03-18T01:47:21.450Z","avatar_url":"https://github.com/Illumina.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Platinum Genomes\n\nThis repo contains the Platinum Genomes small variant truthset for samples NA12878 (also known as hg001) and NA12877.\nPlatinum Genomes truthset variants were validated using haplotype inheritance information through a well studied \n17-member pedigree (CEPH 1463).\n\n## Truthsets\n\nTruthsets are made up of a VCF of validated variant records and a BED file of confident regions. These\nfiles aren't huge (00s of MB) but are too large to play nicely with git and github, here's a few ways to download:\n\n### AWS CLI\n\nTruthset files are stored in an AWS S3 bucket called `platinum-genomes`, one way to download is via the [AWS CLI](https://aws.amazon.com/cli/):\n\n```bash\naws s3 cp s3://platinum-genomes/2017-1.0 pg2017 --recursive\n```\n\nTo download without AWS credentials, add the `--no-sign-request` flag. You can also explore the bucket and download individual files with this [S3 bucket display](https://illumina.github.io/PlatinumGenomes/).\n\n### wget\n\nAlternatively, use `wget` or similar with the [file URIs in this repo](files/), e.g.:\n\n```bash\nwget -xi files/2017-1.0.files\n```\n\nYou can then use the relevant md5 checksum in each release to validate data integrity. \n\nFinally, truthset files can also be downloaded via [FTP](ftp://platgene_ro:''@ussd-ftp.illumina.com/), e.g.:\n\n```sh\nwget ftp://platgene_ro:''@ussd-ftp.illumina.com/2017-1.0/hg38/small_variants/NA12878/NA12878.vcf.gz\n```\n\n## Usage\n\nTo compare a VCF against these truthsets, we recommend using [hap.py](https://github.com/Illumina/hap.py) which\nperforms a sophisticated haplotype comparison rather than a simpler tool such as `bcftools isec`.\n\nApplications wrapping hap.py and containing these truthsets are available on the following platforms:\n* BaseSpace Sequence Hub ([Hap.py Benchmarking](https://basespace.illumina.com/apps/3067064/Hap-py-Benchmarking) and [VCAT](https://basespace.illumina.com/apps/2106105/Variant-Calling-Assessment-Tool))\n* PrecisionFDA (GA4GH Benchmarking)\n\n## Details\n\nSee the attached [wiki](../../wiki) for technical information.\n\n## Raw data\n\nSequencing data for NA12878, NA12877 and samples NA12889-NA12892 (grandparents) are available through\nthe ENA:\n* [ENA Study: PRJEB3381](https://www.ebi.ac.uk/ena/data/view/PRJEB3381)\n\nBaseSpace users can access this data via a shared BaseSpace project:\n* [BaseSpace project share](https://basespace.illumina.com/s/2K7LqNG7Mt1h)\n\nSequencing data for the remaining pedigree members is not consented for public release and so is \nmade available through the dbGaP database:\n* [dbGaP: phs001224.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001224.v1.p1)\n\n## Issues\n\nPlease open an [issue](/../../issues/) for comments, issues and other feedback.\n\n## Citation\n\nFor further information or to cite Platinum Genomes resources, see:\n* Eberle, MA _et al._ (2017) A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. _Genome Research_, 27:157-164. doi:[10.1101/gr.210500.116](http://dx.doi.org/10.1101/gr.210500.116)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fillumina%2Fplatinumgenomes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fillumina%2Fplatinumgenomes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fillumina%2Fplatinumgenomes/lists"}