payload: {"action":"closed","issue":{"url":"https://api.github.com/repos/Nealelab/UK_Biobank_GWAS/issues/24","repository_url":"https://api.github.com/repos/Nealelab/UK_Biobank_GWAS","labels_url":"https://api.github.com/repos/Nealelab/UK_Biobank_GWAS/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/Nealelab/UK_Biobank_GWAS/issues/24/comments","events_url":"https://api.github.com/repos/Nealelab/UK_Biobank_GWAS/issues/24/events","html_url":"https://github.com/Nealelab/UK_Biobank_GWAS/issues/24","id":538288840,"node_id":"MDU6SXNzdWU1MzgyODg4NDA=","number":24,"title":"Unrelatedness in sample QC?","user":{"login":"Ojami","id":13262628,"node_id":"MDQ6VXNlcjEzMjYyNjI4","avatar_url":"https://avatars0.githubusercontent.com/u/13262628?v=4","gravatar_id":"","url":"https://api.github.com/users/Ojami","html_url":"https://github.com/Ojami","followers_url":"https://api.github.com/users/Ojami/followers","following_url":"https://api.github.com/users/Ojami/following{/other_user}","gists_url":"https://api.github.com/users/Ojami/gists{/gist_id}","starred_url":"https://api.github.com/users/Ojami/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ojami/subscriptions","organizations_url":"https://api.github.com/users/Ojami/orgs","repos_url":"https://api.github.com/users/Ojami/repos","events_url":"https://api.github.com/users/Ojami/events{/privacy}","received_events_url":"https://api.github.com/users/Ojami/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2019-12-16T09:29:37Z","updated_at":"2019-12-16T15:47:45Z","closed_at":"2019-12-16T15:47:45Z","author_association":"NONE","body":"Hi,\r\n\r\nI have a general question regarding relatedness in sample QC. As mentioned here (https://github.com/Nealelab/UK_Biobank_GWAS#imputed-v3-sample-qc) `Used.in.pca.calculation` filter should remove related individuals from the sample. However, when I remove individuals based on this filter and other filters (e.g. sex chromosome aneuploidy and White.british.ancestry) from the relatedness pairs (fetched via `ukbgene rel`), there still ~28800 pairs of related individuals.\r\nCan you please help me to understand this? Am I doing something wrong here?\r\n\r\nThanks!"}}
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