{"action":"closed","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/216","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/216/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/216/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/216/events","html_url":"https://github.com/samtools/bcftools/issues/216","id":58371544,"number":216,"title":"force bcftools norm to continue when ref is N","user":{"login":"silvia-s","id":9861211,"avatar_url":"https://avatars.githubusercontent.com/u/9861211?v=3","gravatar_id":"","url":"https://api.github.com/users/silvia-s","html_url":"https://github.com/silvia-s","followers_url":"https://api.github.com/users/silvia-s/followers","following_url":"https://api.github.com/users/silvia-s/following{/other_user}","gists_url":"https://api.github.com/users/silvia-s/gists{/gist_id}","starred_url":"https://api.github.com/users/silvia-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/silvia-s/subscriptions","organizations_url":"https://api.github.com/users/silvia-s/orgs","repos_url":"https://api.github.com/users/silvia-s/repos","events_url":"https://api.github.com/users/silvia-s/events{/privacy}","received_events_url":"https://api.github.com/users/silvia-s/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-20T15:57:17Z","updated_at":"2015-02-20T16:09:59Z","closed_at":"2015-02-20T16:09:59Z","body":"Hi there,\r\nI am using bcftools norm to check if REF alleles in a vcf file match the reference fasta genome. However, when the tool finds an N in the reference fasta file (e.g. \"Reference allele mismatch at Y:272182 .. 'N' vs 'G'), it just stops. Would it be possible to add an option to force bcftools norm continuing its scan instead?\r\nThanks a lot for your help!\r\n"}}