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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
317 stars 120 forks source link

Consider adding DIVAS background panels #550

Open schelhorn opened 8 years ago

schelhorn commented 8 years ago

There is a new collection of background panels out; it would be nice to have their variants annotated in GEMINI.

The Disease Variant Store provides information on genetic variants observed in various disease populations. Users can quickly obtain frequencies, functional annotations, and known disease annotations by performing simple queries.

1000 Genomes Project Phase 3 1KGp3 2504 http://www.1000genomes.org/ NHLBI GO Exome Sequencing Project ESP6500 6503 https://esp.gs.washington.edu/drupal/ Exome Aggregation Consortium ExAC 63352 http://exac.broadinstitute.org/ Genetic Epidemiology Research on Adult Health and Aging GERA 78486 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000674 GRU GO-ESP Chronic Obstructive Pulmonary Disease GRU_COPD 337 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000291 GRU Drug Resistant Hypertension in African Americans GRU_DRH 91 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000442 GRU Familial Amyotrophic Lateral Sclerosis GRU_FALS 247 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000101 GRU Familial Intracranial Aneurysm GRU_FIA 32 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000636 GRU Inherited Muscle Disease GRU_IMD 248 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000655 GRU Rare Mendelian Disease in Old Order Amish and Mennonite Patients GRU_Plain 105 http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000623 Supercentenarian SuperCent 17 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0112430 UK10K Whole Genome Cohorts UK10K_ALSPAC, UK10K_TWINS 2432 http://www.uk10k.org/studies/cohorts.html Scripps Wellderly Wellderly 534 http://www.stsiweb.org/wellderly/ Functional Impact Sources

DIVAS uses snpEff for all functional impact annotations, using GRCh37.75 as the reference genome. We also provide predictions based on various tools, such as SIFT and MutationAssessor; precomputed by dbNSFP.

DIVAS contains variants for 58434 genes, pseudogenes, and other non-coding regions, for which transcripts are available from either ENSEMBL or RefSeq.

brentp commented 8 years ago

This would be useful. It's not clear from the site what the usage restrictions are. We'd have to make an API call for each variant, so that would be pretty slow.