{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/agg/issues/1","repository_url":"https://api.github.com/repos/Illumina/agg","labels_url":"https://api.github.com/repos/Illumina/agg/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/agg/issues/1/comments","events_url":"https://api.github.com/repos/Illumina/agg/issues/1/events","html_url":"https://github.com/Illumina/agg/issues/1","id":120185123,"number":1,"title":"proper handling of haploid regions","user":{"login":"jaredo","id":349198,"avatar_url":"https://avatars.githubusercontent.com/u/349198?v=3","gravatar_id":"","url":"https://api.github.com/users/jaredo","html_url":"https://github.com/jaredo","followers_url":"https://api.github.com/users/jaredo/followers","following_url":"https://api.github.com/users/jaredo/following{/other_user}","gists_url":"https://api.github.com/users/jaredo/gists{/gist_id}","starred_url":"https://api.github.com/users/jaredo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaredo/subscriptions","organizations_url":"https://api.github.com/users/jaredo/orgs","repos_url":"https://api.github.com/users/jaredo/repos","events_url":"https://api.github.com/users/jaredo/events{/privacy}","received_events_url":"https://api.github.com/users/jaredo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Illumina/agg/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-12-03T14:37:47Z","updated_at":"2016-05-19T21:02:14Z","closed_at":null,"body":"Agg currently assumes everything is diploid.  This behaviour is obviously incorrect for chrY, chrM and male chrX.  We should be able to provide a bed file to `agg genotype` specifying the ploidy of regions.\r\n"},"comment":{"url":"https://api.github.com/repos/Illumina/agg/issues/comments/220451120","html_url":"https://github.com/Illumina/agg/issues/1#issuecomment-220451120","issue_url":"https://api.github.com/repos/Illumina/agg/issues/1","id":220451120,"user":{"login":"jaredo","id":349198,"avatar_url":"https://avatars.githubusercontent.com/u/349198?v=3","gravatar_id":"","url":"https://api.github.com/users/jaredo","html_url":"https://github.com/jaredo","followers_url":"https://api.github.com/users/jaredo/followers","following_url":"https://api.github.com/users/jaredo/following{/other_user}","gists_url":"https://api.github.com/users/jaredo/gists{/gist_id}","starred_url":"https://api.github.com/users/jaredo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaredo/subscriptions","organizations_url":"https://api.github.com/users/jaredo/orgs","repos_url":"https://api.github.com/users/jaredo/repos","events_url":"https://api.github.com/users/jaredo/events{/privacy}","received_events_url":"https://api.github.com/users/jaredo/received_events","type":"User","site_admin":false},"created_at":"2016-05-19T21:02:14Z","updated_at":"2016-05-19T21:02:14Z","body":"Interim fix:\r\n\r\n```\r\n$ head b37.ploidy.tab\r\nchrX 1 60000 M 1\r\nchrX 2699521 154931043 M 1\r\nchrY 1 59373566 M 1\r\nchrY 1 59373566 F 0\r\nchrM 1 16569 M 1\r\nchrM 1 16569 F 1\r\n \r\n$ head sex.txt\r\nsample1 F\r\nsample2 F\r\nsample3 M\r\n \r\n$ bcftools +fixploidy $input --  -s sex.txt -p ploidy.tab | bcftools +fill-AN-AC | bcftools view -Ob -o $output\r\n ```\r\nwill produce correct calls."}}