{"action":"created","issue":{"url":"https://api.github.com/repos/ClinGen/clincoded/issues/683","repository_url":"https://api.github.com/repos/ClinGen/clincoded","labels_url":"https://api.github.com/repos/ClinGen/clincoded/issues/683/labels{/name}","comments_url":"https://api.github.com/repos/ClinGen/clincoded/issues/683/comments","events_url":"https://api.github.com/repos/ClinGen/clincoded/issues/683/events","html_url":"https://github.com/ClinGen/clincoded/issues/683","id":155850192,"number":683,"title":"Create Population Tab on Variant Curation Evidence Hub pages","user":{"login":"wrightmw","id":15131169,"avatar_url":"https://avatars.githubusercontent.com/u/15131169?v=3","gravatar_id":"","url":"https://api.github.com/users/wrightmw","html_url":"https://github.com/wrightmw","followers_url":"https://api.github.com/users/wrightmw/followers","following_url":"https://api.github.com/users/wrightmw/following{/other_user}","gists_url":"https://api.github.com/users/wrightmw/gists{/gist_id}","starred_url":"https://api.github.com/users/wrightmw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wrightmw/subscriptions","organizations_url":"https://api.github.com/users/wrightmw/orgs","repos_url":"https://api.github.com/users/wrightmw/repos","events_url":"https://api.github.com/users/wrightmw/events{/privacy}","received_events_url":"https://api.github.com/users/wrightmw/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ClinGen/clincoded/labels/in%20progress","name":"in progress","color":"ededed"},{"url":"https://api.github.com/repos/ClinGen/clincoded/labels/variant%20curation%20interface","name":"variant curation interface","color":"1791B3"}],"state":"open","locked":false,"assignee":{"login":"jimmyzhen","id":6956310,"avatar_url":"https://avatars.githubusercontent.com/u/6956310?v=3","gravatar_id":"","url":"https://api.github.com/users/jimmyzhen","html_url":"https://github.com/jimmyzhen","followers_url":"https://api.github.com/users/jimmyzhen/followers","following_url":"https://api.github.com/users/jimmyzhen/following{/other_user}","gists_url":"https://api.github.com/users/jimmyzhen/gists{/gist_id}","starred_url":"https://api.github.com/users/jimmyzhen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimmyzhen/subscriptions","organizations_url":"https://api.github.com/users/jimmyzhen/orgs","repos_url":"https://api.github.com/users/jimmyzhen/repos","events_url":"https://api.github.com/users/jimmyzhen/events{/privacy}","received_events_url":"https://api.github.com/users/jimmyzhen/received_events","type":"User","site_admin":false},"milestone":null,"comments":11,"created_at":"2016-05-19T22:32:04Z","updated_at":"2016-06-15T04:26:17Z","closed_at":null,"body":"There will be a tab on the Variant Curation Evidence Hub pages that will show the allele frequency (and other associated fields) in specific populations. These population frequency data are generated by GO-ESP (ESP), ExAC, and 1,000Genomes (1KG). The ACMG guidelines only require ESP, ExAC and 1KG as a minimum and so for the MVP we will only be supplying these, but future iterations will no doubt include additional data sources that provide allele frequency data for other specific populations. We are looking into potentially downloading the ESP, ExAC and 1KG data we require all in one go via the Variant Effect Predictor (VEP), however if this is not possible then we will have to source from each of these sources separately."},"comment":{"url":"https://api.github.com/repos/ClinGen/clincoded/issues/comments/226084857","html_url":"https://github.com/ClinGen/clincoded/issues/683#issuecomment-226084857","issue_url":"https://api.github.com/repos/ClinGen/clincoded/issues/683","id":226084857,"user":{"login":"jimmyzhen","id":6956310,"avatar_url":"https://avatars.githubusercontent.com/u/6956310?v=3","gravatar_id":"","url":"https://api.github.com/users/jimmyzhen","html_url":"https://github.com/jimmyzhen","followers_url":"https://api.github.com/users/jimmyzhen/followers","following_url":"https://api.github.com/users/jimmyzhen/following{/other_user}","gists_url":"https://api.github.com/users/jimmyzhen/gists{/gist_id}","starred_url":"https://api.github.com/users/jimmyzhen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimmyzhen/subscriptions","organizations_url":"https://api.github.com/users/jimmyzhen/orgs","repos_url":"https://api.github.com/users/jimmyzhen/repos","events_url":"https://api.github.com/users/jimmyzhen/events{/privacy}","received_events_url":"https://api.github.com/users/jimmyzhen/received_events","type":"User","site_admin":false},"created_at":"2016-06-15T04:26:17Z","updated_at":"2016-06-15T04:26:17Z","body":"Hi @selinad, @wrightmw, @kilodalton, @kgliu0101, @mrmin123,\r\n\r\nSo far for the Population tab UI, I have done the following:\r\n1) Pulling data from myvariant.info to populate the **Allele Count**, **Allele Number**, **Number of Homozygotes** columns for all populations in the ExAc table.\r\n2) Pulling data from VEP to populate the **Allele Frequency** column for all populations in the ExAC table. This is implemented in such way because the ExAC allele frequency data is not always present in the myvariant.info API response for certain variants, even though frequency data is present at ExAC and in the VEP API response. See table below for reference and compare the presence/absence of `{dbnsfp: {exac: {...}}}` in the myvariant.info responses.\r\n\r\n| Datasource | Missing allele frequency in myvariant.info | Has allele frequency in myvariant.info |\r\n|---|---|---|\r\n| myvariant.info  | http://myvariant.info/v1/variant/chr15:g.67358465C%3ET | http://myvariant.info/v1/variant/chr7:g.107423522C%3EG |\r\n| VEP | http://rest.ensembl.org/vep/human/id/rs144374592?content-type=application/json | http://rest.ensembl.org/vep/human/id/rs386833446?content-type=application/json |\r\n| ExAC | http://exac.broadinstitute.org/variant/15-67358465-C-T | http://exac.broadinstitute.org/variant/7-107423522-C-G |\r\n\r\n3) Pulling data from VEP to populate the **Allele Frequency (count)** and **Genotype Frequency (count)** columns for all populations in the 1000G table (e.g. http://rest.ensembl.org/variation/human/rs1801133?content-type=application/json;pops=1;population_genotypes=1).\r\n4) Pulling data from myvariant.info to populate the **Allele Count** and **Genotype Count** columns for all populations in the ESP table. Because the ESP allele and genotype data is not always present in the myvariant.info API responses for certain variants, we have decided to display a message in the table similar to \"Variant information can not be found. Please see [[link]](url)\" when ESP data is unavailable. See table below to compare the presence/absence of `{evs: {...}}` in the myvariant.info responses.\r\n\r\n| Missing ESP data in myvariant.info | Has ESP data in myvariant.info |\r\n|---|---|\r\n| http://myvariant.info/v1/variant/chr7:g.107423522C%3EG, http://myvariant.info/v1/variant/chr7:g.107423741C%3ET | http://myvariant.info/v1/variant/chr15:g.67358465C%3ET |\r\n\r\nWhat I have not implemented:\r\n1) The supposedly pre-populated fields in the **Highest Minor Allele Frequency** section on the Population tab.\r\n2) Replace the dashes (e.g. \"--\") with gray boxes for fields that are not present in the API responses.\r\n\r\nKnown issues:\r\n1) Neither myvariant.info nor VEP has the ExAC \"Filter Status\" and \"Median Coverage\" data in their responses.\r\n\r\nPlease feel free to ask me any questions in this regard."}}
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