{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/879","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/879/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/879/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/879/events","html_url":"https://github.com/samtools/bcftools/issues/879","id":358247551,"node_id":"MDU6SXNzdWUzNTgyNDc1NTE=","number":879,"title":"When merging, remove SNPs that do not match the REF allele, without considering ALT alleles","user":{"login":"MrLocuace","id":20564007,"node_id":"MDQ6VXNlcjIwNTY0MDA3","avatar_url":"https://avatars3.githubusercontent.com/u/20564007?v=4","gravatar_id":"","url":"https://api.github.com/users/MrLocuace","html_url":"https://github.com/MrLocuace","followers_url":"https://api.github.com/users/MrLocuace/followers","following_url":"https://api.github.com/users/MrLocuace/following{/other_user}","gists_url":"https://api.github.com/users/MrLocuace/gists{/gist_id}","starred_url":"https://api.github.com/users/MrLocuace/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MrLocuace/subscriptions","organizations_url":"https://api.github.com/users/MrLocuace/orgs","repos_url":"https://api.github.com/users/MrLocuace/repos","events_url":"https://api.github.com/users/MrLocuace/events{/privacy}","received_events_url":"https://api.github.com/users/MrLocuace/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-09-08T00:32:25Z","updated_at":"2018-09-20T16:10:33Z","closed_at":"2018-09-20T16:10:33Z","author_association":"NONE","body":"Hello, I have vcf files from 2 populations which I want to merge. In the REF and ALT columns I have situations like this one:\r\n\r\npop1:\r\n\r\n    ID   REF    ALT\r\n    rs1    A    C\r\n    rs2    C    .\r\n\r\npop2:\r\n\r\nID   REF    ALT\r\nrs1    C   A\r\nrs2    C   T\r\n\r\nI want to remove SNPs that do not match the REF allele, but not to remove SNPs where the mismatch is due to \".\" in ALT. How to do it with bcftools?. Thank you !\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/bcftools/issues/comments/423241957","html_url":"https://github.com/samtools/bcftools/issues/879#issuecomment-423241957","issue_url":"https://api.github.com/repos/samtools/bcftools/issues/879","id":423241957,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMzI0MTk1Nw==","user":{"login":"MrLocuace","id":20564007,"node_id":"MDQ6VXNlcjIwNTY0MDA3","avatar_url":"https://avatars3.githubusercontent.com/u/20564007?v=4","gravatar_id":"","url":"https://api.github.com/users/MrLocuace","html_url":"https://github.com/MrLocuace","followers_url":"https://api.github.com/users/MrLocuace/followers","following_url":"https://api.github.com/users/MrLocuace/following{/other_user}","gists_url":"https://api.github.com/users/MrLocuace/gists{/gist_id}","starred_url":"https://api.github.com/users/MrLocuace/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MrLocuace/subscriptions","organizations_url":"https://api.github.com/users/MrLocuace/orgs","repos_url":"https://api.github.com/users/MrLocuace/repos","events_url":"https://api.github.com/users/MrLocuace/events{/privacy}","received_events_url":"https://api.github.com/users/MrLocuace/received_events","type":"User","site_admin":false},"created_at":"2018-09-20T16:10:33Z","updated_at":"2018-09-20T16:10:33Z","author_association":"NONE","body":"Thank you @finswimmer !"}}
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