{"action":"created","issue":{"url":"https://api.github.com/repos/chrchang/plink-ng/issues/29","repository_url":"https://api.github.com/repos/chrchang/plink-ng","labels_url":"https://api.github.com/repos/chrchang/plink-ng/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/chrchang/plink-ng/issues/29/comments","events_url":"https://api.github.com/repos/chrchang/plink-ng/issues/29/events","html_url":"https://github.com/chrchang/plink-ng/issues/29","id":139198256,"number":29,"title":"lfile 3+ different alleles error","user":{"login":"dwaggott","id":3149944,"avatar_url":"https://avatars.githubusercontent.com/u/3149944?v=3","gravatar_id":"","url":"https://api.github.com/users/dwaggott","html_url":"https://github.com/dwaggott","followers_url":"https://api.github.com/users/dwaggott/followers","following_url":"https://api.github.com/users/dwaggott/following{/other_user}","gists_url":"https://api.github.com/users/dwaggott/gists{/gist_id}","starred_url":"https://api.github.com/users/dwaggott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwaggott/subscriptions","organizations_url":"https://api.github.com/users/dwaggott/orgs","repos_url":"https://api.github.com/users/dwaggott/repos","events_url":"https://api.github.com/users/dwaggott/events{/privacy}","received_events_url":"https://api.github.com/users/dwaggott/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2016-03-08T07:07:03Z","updated_at":"2016-05-26T09:16:35Z","closed_at":null,"body":"I'm struggling getting some illumina genotypes to load. I've converted the gtreports to lgen format but keep getting the 3+ allele error. In the example below all that's there is A and 0. Specifying `--missing-genotype 0` didn't seem to help.\r\n\r\n[mega.map](https://gist.github.com/e40fd5af97308ab94d8b)\r\n[mega.fam](https://gist.github.com/762c9d631fba28a91a2d)\r\n[mega.lgen](https://gist.github.com/d8c59edbe97ba65e8c0)\r\n\r\n`plink --lfile mega`\r\nError: Variant '1:10001102-G-T' in .lgen file has 3+ different alleles\r\n\r\nThis was using code from Feb 2016. Using a version from 2014 worked."},"comment":{"url":"https://api.github.com/repos/chrchang/plink-ng/issues/comments/221819644","html_url":"https://github.com/chrchang/plink-ng/issues/29#issuecomment-221819644","issue_url":"https://api.github.com/repos/chrchang/plink-ng/issues/29","id":221819644,"user":{"login":"ALSHAWI","id":18593179,"avatar_url":"https://avatars.githubusercontent.com/u/18593179?v=3","gravatar_id":"","url":"https://api.github.com/users/ALSHAWI","html_url":"https://github.com/ALSHAWI","followers_url":"https://api.github.com/users/ALSHAWI/followers","following_url":"https://api.github.com/users/ALSHAWI/following{/other_user}","gists_url":"https://api.github.com/users/ALSHAWI/gists{/gist_id}","starred_url":"https://api.github.com/users/ALSHAWI/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ALSHAWI/subscriptions","organizations_url":"https://api.github.com/users/ALSHAWI/orgs","repos_url":"https://api.github.com/users/ALSHAWI/repos","events_url":"https://api.github.com/users/ALSHAWI/events{/privacy}","received_events_url":"https://api.github.com/users/ALSHAWI/received_events","type":"User","site_admin":false},"created_at":"2016-05-26T09:16:35Z","updated_at":"2016-05-26T09:16:35Z","body":"Hi every one\r\n\r\nI tried to make PED&MAP files by PLINK from three files that I made it .lgen ,.map &.fam So,error appeared\r\n\r\nError: Variant 'ARS-BFGL-BAC-27364' in .lgen file has 3+ different alleles.\r\n\r\nSo,the command that I used it ./plink --lfile rustaqi22 --cow --recode\r\n\r\nMoreover,example below of rows of my .lgen file\r\n\r\nRustaqi 88 ARS-BFGL-BAC-10172 B B Rustaqi 88 ARS-BFGL-BAC-1020 A B Rustaqi 88 ARS-BFGL-BAC-10245 B B\r\n\r\nCould any one advice how to deal with this point?\r\n\r\nThanks"}}
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