30:[{"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}] 2e:{"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.

","pinned":false,"hidden":false,"mode":"md"},{"id":5,"value":"hits = FileAttachment(\"hits@1.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"## QA/QC","pinned":false,"hidden":false,"mode":"md"},{"id":14,"value":"

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"},{"id":49,"value":"V = require(\"https://episphere.github.io/vcf/vcf.js\")","pinned":true,"hidden":false,"mode":"ojs"},{"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"},{"id":57,"value":"hit108 = v108.query(\"5:77155397\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":60,"value":"hit108.hit[0]","pinned":true,"hidden":false,"mode":"ojs"},{"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"},{"id":72,"value":"### Aaron checking a different position: chr1:100880328","pinned":false,"hidden":false,"mode":"md"},{"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"},{"id":87,"value":"chr1.query(\"1:18807339\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":93,"value":"chr1.cols.length","pinned":true,"hidden":false,"mode":"ojs"},{"id":100,"value":"cliceCols = chr1.cols.slice(-10)","pinned":false,"hidden":false,"mode":"ojs"},{"id":104,"value":"chr1.query(\"1:10505\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":117,"value":"individuals = chr1.cols.slice(9)","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W30","stdlib":"1","titling":"auto"}