{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/412","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/412/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/412/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/412/events","html_url":"https://github.com/samtools/bcftools/issues/412","id":148780014,"number":412,"title":"merge issues with monoallelic positions","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":4,"created_at":"2016-04-15T22:02:37Z","updated_at":"2016-04-19T20:57:28Z","closed_at":null,"body":"I'm not quite sure how to deal with the following scenario.\r\n\r\nI'm merging lots of vcf's. Some vcf's have the REF homozygotes called with no ALT specified. When merging using `-m none`, positions with no ALT don't seem to get merged properly. i.e. each observed genotype at the same position ends up on it's own line.\r\n\r\nHow might I avoid this so that the merging creates one line per position. I guess this requires two pieces of logic. First that the mono-allelics get merged and second that mono-allelics can be merged with bi-allelics.\r\n\r\nIf this can't be done via merging is there a way to resolve and collapse the variants using `norm`. Conventional multi-allelics should be split across multiple lines.\r\n\r\nexample output:\r\nhttps://gist.github.com/655c3c579098aa41881c15c68a5aa5cd"},"comment":{"url":"https://api.github.com/repos/samtools/bcftools/issues/comments/212125609","html_url":"https://github.com/samtools/bcftools/issues/412#issuecomment-212125609","issue_url":"https://api.github.com/repos/samtools/bcftools/issues/412","id":212125609,"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},"created_at":"2016-04-19T20:57:28Z","updated_at":"2016-04-19T20:57:28Z","body":"Output looks wonky. Each GT at the same position is now on it's own line.\r\n\r\nhttps://gist.github.com/cf8c16830b71efea264d577eaf0e03ee"}}