2c:null 2d:["$","title",null,{"children":"PRS313 | Jonas Almeida | Observable"}] 32:[{"id":"f4fc042af3fb512119d6c701b8dfea5027297893eac594b180ac7300ad4e44a4432c2931e40a59c2d9f5e15851d669c513482f129a0f8b52c4a66c4578b5394c","href":"https://static.observableusercontent.com/files/f4fc042af3fb512119d6c701b8dfea5027297893eac594b180ac7300ad4e44a4432c2931e40a59c2d9f5e15851d669c513482f129a0f8b52c4a66c4578b5394c","name":"hits.json","type":"application/json","lastModified":1711459705551.377,"size":2476293},{"id":"f4fc042af3fb512119d6c701b8dfea5027297893eac594b180ac7300ad4e44a4432c2931e40a59c2d9f5e15851d669c513482f129a0f8b52c4a66c4578b5394c","href":"https://static.observableusercontent.com/files/f4fc042af3fb512119d6c701b8dfea5027297893eac594b180ac7300ad4e44a4432c2931e40a59c2d9f5e15851d669c513482f129a0f8b52c4a66c4578b5394c","name":"hits@1.json","type":"application/json","lastModified":1711567662592.255,"size":2476293}] 30:{"id":"bcb30d3793c45e8d","slug":"prs313","title":"PRS313","thumbnail":"81bd9a151c94426727905cc784031616deeb918e615b2529f863d1aafce54ef5","access_level":"public","create_time":"$D2024-03-26T13:17:35.356Z","update_time":"$D2024-03-27T20:43:50.622Z","view_time":null,"first_public_time":"$D2024-03-26T13:21:22.868Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"0f2e596d5bd6ef6e","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":"starter_2024"},"version":125,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null},{"type":"individual","id":"352a9430837886b4","login":"jeyabbalas","name":"Jeya Balaji Balasubramanian","avatar_url":"https://avatars-next.observableusercontent.com/80f51d00c7e14ae878fca50bb97e3d82c91a9c13d88c71a3bd41f878c83c135e","tier":null}],"members":[{"type":"team","id":"0f2e596d5bd6ef6e","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":"starter_2024","role":"editor"},{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"PRS313","cells":[{"id":0,"value":"# PRS313\n\nHow well can we do reference-free imputation of PRS313 variant panel by training an neural network model with 1000genome data? The range request approach will use epiSPhere's VCF library.

A. Missing genotypes?

\n Some hits, like #108, do not have complete records (#108 only has 597-8 individuals), and quite a few have no hits. I wonder if the format of master VCF files excludes subjects if all remaining genotypes are \"0|0\". Let's have a look at that position:\n

","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":49,"value":"V = require(\"https://episphere.github.io/vcf/vcf.js\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"v108 = V.Vcf(\n \"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr5.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"hit108 = v108.query(\"5:77155397\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":60,"value":"hit108.hit[0]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":62,"value":"Confirmed that PRS313#108 only lists 597-8 = 589 indiviuals. So far it looks the VCF library is correctly reading from this 1000genome project entry.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":72,"value":"### Aaron checking a different position: chr1:100880328","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":75,"value":"chr1 = V.Vcf(\n \"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz\"\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":87,"value":"chr1.query(\"1:18807339\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"chr1.cols.length","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":100,"value":"cliceCols = chr1.cols.slice(-10)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":104,"value":"chr1.query(\"1:10505\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":117,"value":"individuals = chr1.cols.slice(9)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1"}} 31:"$30:body"