{"action":"created","issue":{"url":"https://api.github.com/repos/choishingwan/PRSice/issues/125","repository_url":"https://api.github.com/repos/choishingwan/PRSice","labels_url":"https://api.github.com/repos/choishingwan/PRSice/issues/125/labels{/name}","comments_url":"https://api.github.com/repos/choishingwan/PRSice/issues/125/comments","events_url":"https://api.github.com/repos/choishingwan/PRSice/issues/125/events","html_url":"https://github.com/choishingwan/PRSice/issues/125","id":470398242,"node_id":"MDU6SXNzdWU0NzAzOTgyNDI=","number":125,"title":"Question about clumping based on BGEN file","user":{"login":"aholleman","id":24921315,"node_id":"MDQ6VXNlcjI0OTIxMzE1","avatar_url":"https://avatars3.githubusercontent.com/u/24921315?v=4","gravatar_id":"","url":"https://api.github.com/users/aholleman","html_url":"https://github.com/aholleman","followers_url":"https://api.github.com/users/aholleman/followers","following_url":"https://api.github.com/users/aholleman/following{/other_user}","gists_url":"https://api.github.com/users/aholleman/gists{/gist_id}","starred_url":"https://api.github.com/users/aholleman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aholleman/subscriptions","organizations_url":"https://api.github.com/users/aholleman/orgs","repos_url":"https://api.github.com/users/aholleman/repos","events_url":"https://api.github.com/users/aholleman/events{/privacy}","received_events_url":"https://api.github.com/users/aholleman/received_events","type":"User","site_admin":false},"labels":[{"id":418908649,"node_id":"MDU6TGFiZWw0MTg5MDg2NDk=","url":"https://api.github.com/repos/choishingwan/PRSice/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":{"login":"choishingwan","id":1259746,"node_id":"MDQ6VXNlcjEyNTk3NDY=","avatar_url":"https://avatars2.githubusercontent.com/u/1259746?v=4","gravatar_id":"","url":"https://api.github.com/users/choishingwan","html_url":"https://github.com/choishingwan","followers_url":"https://api.github.com/users/choishingwan/followers","following_url":"https://api.github.com/users/choishingwan/following{/other_user}","gists_url":"https://api.github.com/users/choishingwan/gists{/gist_id}","starred_url":"https://api.github.com/users/choishingwan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choishingwan/subscriptions","organizations_url":"https://api.github.com/users/choishingwan/orgs","repos_url":"https://api.github.com/users/choishingwan/repos","events_url":"https://api.github.com/users/choishingwan/events{/privacy}","received_events_url":"https://api.github.com/users/choishingwan/received_events","type":"User","site_admin":false},"assignees":[{"login":"choishingwan","id":1259746,"node_id":"MDQ6VXNlcjEyNTk3NDY=","avatar_url":"https://avatars2.githubusercontent.com/u/1259746?v=4","gravatar_id":"","url":"https://api.github.com/users/choishingwan","html_url":"https://github.com/choishingwan","followers_url":"https://api.github.com/users/choishingwan/followers","following_url":"https://api.github.com/users/choishingwan/following{/other_user}","gists_url":"https://api.github.com/users/choishingwan/gists{/gist_id}","starred_url":"https://api.github.com/users/choishingwan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choishingwan/subscriptions","organizations_url":"https://api.github.com/users/choishingwan/orgs","repos_url":"https://api.github.com/users/choishingwan/repos","events_url":"https://api.github.com/users/choishingwan/events{/privacy}","received_events_url":"https://api.github.com/users/choishingwan/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2019-07-19T15:51:47Z","updated_at":"2019-07-19T20:39:34Z","closed_at":null,"author_association":"NONE","body":"Hi Sam,\r\n\r\nI'm running PRSice (v2.2.3) using a BGEN file with genotype probabilities as the target. When I don't include an external LD reference, PRSice computes LD by hard coding the BGEN file; I'm using --hard-thres 0.80 (and NOT using --hard), and this results in 9,203 SNPs remaining after clumping (see attached file with 'noLDref' in name). I've also run PRSice using this same BGEN file, but with an external LD reference that is actually a Plink1.9 bfile with the exact same samples and variants as in the BGEN file, and with hard genotype calls made based on the same GP threshold of 0.80; this results in 29,841 SNPs remaining after clumping (see attached file with 'LDrefDS' in name). I don't understand why the number of SNPs after clumping is so different. I would think they'd be pretty much the same number, since the number of SNPs just before clumping is exactly the same in both cases, and in both cases LD is calculated based on the exact same samples, the exact same variants, with the exact same GP threshold applied for hard calling genotypes. Perhaps I'm overlooking something? I'm hoping you can help me wrap my head around this.\r\n\r\nThanks,\r\nAaron\r\n\r\n[DSAffyImputed_403_CHDplusTOFtrain_maf30inTrain_geno02_noMHC_Sex_just.lnOR_BGENdosages_noLDref_v2.2.3.log](https://github.com/choishingwan/PRSice/files/3411783/DSAffyImputed_403_CHDplusTOFtrain_maf30inTrain_geno02_noMHC_Sex_just.lnOR_BGENdosages_noLDref_v2.2.3.log)\r\n[DSAffyImputed_403_CHDplusTOFtrain_maf30inTrain_geno02_noMHC_Sex_just.lnOR_BGENdosages_LDrefDS_v2.2.3.log](https://github.com/choishingwan/PRSice/files/3411785/DSAffyImputed_403_CHDplusTOFtrain_maf30inTrain_geno02_noMHC_Sex_just.lnOR_BGENdosages_LDrefDS_v2.2.3.log)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/choishingwan/PRSice/issues/comments/513370108","html_url":"https://github.com/choishingwan/PRSice/issues/125#issuecomment-513370108","issue_url":"https://api.github.com/repos/choishingwan/PRSice/issues/125","id":513370108,"node_id":"MDEyOklzc3VlQ29tbWVudDUxMzM3MDEwOA==","user":{"login":"aholleman","id":24921315,"node_id":"MDQ6VXNlcjI0OTIxMzE1","avatar_url":"https://avatars3.githubusercontent.com/u/24921315?v=4","gravatar_id":"","url":"https://api.github.com/users/aholleman","html_url":"https://github.com/aholleman","followers_url":"https://api.github.com/users/aholleman/followers","following_url":"https://api.github.com/users/aholleman/following{/other_user}","gists_url":"https://api.github.com/users/aholleman/gists{/gist_id}","starred_url":"https://api.github.com/users/aholleman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aholleman/subscriptions","organizations_url":"https://api.github.com/users/aholleman/orgs","repos_url":"https://api.github.com/users/aholleman/repos","events_url":"https://api.github.com/users/aholleman/events{/privacy}","received_events_url":"https://api.github.com/users/aholleman/received_events","type":"User","site_admin":false},"created_at":"2019-07-19T20:39:34Z","updated_at":"2019-07-19T20:39:34Z","author_association":"NONE","body":"No problem. Thanks!\n\n________________________________\nFrom: Shing Wan Choi <notifications@github.com>\nSent: Friday, July 19, 2019 4:37:30 PM\nTo: choishingwan/PRSice <PRSice@noreply.github.com>\nCc: Holleman, Aaron <aaron.holleman@emory.edu>; Author <author@noreply.github.com>\nSubject: [External] Re: [choishingwan/PRSice] Question about clumping based on BGEN file (#125)\n\n\nOk, that's clear. I will try to use my samples to see if I can replicate your problems. Please give me some time.\n\n—\nYou are receiving this because you authored the thread.\nReply to this email directly, view it on GitHub<https://github.com/choishingwan/PRSice/issues/125?email_source=notifications&email_token=AF6EJYZRP4JEMAK63GSKDQLQAIQYVA5CNFSM4IFHLCO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2MWLRI#issuecomment-513369541>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AF6EJY2BYUNHBOX3KROJ2LLQAIQYVANCNFSM4IFHLCOQ>.\n\n________________________________\n\nThis e-mail message (including any attachments) is for the sole use of\nthe intended recipient(s) and may contain confidential and privileged\ninformation. If the reader of this message is not the intended\nrecipient, you are hereby notified that any dissemination, distribution\nor copying of this message (including any attachments) is strictly\nprohibited.\n\nIf you have received this message in error, please contact\nthe sender by reply e-mail message and destroy all copies of the\noriginal message (including attachments).\n"}}
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