{"action":"closed","issue":{"url":"https://api.github.com/repos/arq5x/gemini/issues/422","labels_url":"https://api.github.com/repos/arq5x/gemini/issues/422/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/gemini/issues/422/comments","events_url":"https://api.github.com/repos/arq5x/gemini/issues/422/events","html_url":"https://github.com/arq5x/gemini/issues/422","id":65279774,"number":422,"title":"vcftidy error","user":{"login":"nfarzaneh","id":8468050,"avatar_url":"https://avatars.githubusercontent.com/u/8468050?v=3","gravatar_id":"","url":"https://api.github.com/users/nfarzaneh","html_url":"https://github.com/nfarzaneh","followers_url":"https://api.github.com/users/nfarzaneh/followers","following_url":"https://api.github.com/users/nfarzaneh/following{/other_user}","gists_url":"https://api.github.com/users/nfarzaneh/gists{/gist_id}","starred_url":"https://api.github.com/users/nfarzaneh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nfarzaneh/subscriptions","organizations_url":"https://api.github.com/users/nfarzaneh/orgs","repos_url":"https://api.github.com/users/nfarzaneh/repos","events_url":"https://api.github.com/users/nfarzaneh/events{/privacy}","received_events_url":"https://api.github.com/users/nfarzaneh/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-30T19:08:02Z","updated_at":"2015-03-30T20:08:10Z","closed_at":"2015-03-30T20:08:10Z","body":"Hello,\r\n\r\nI get the following error while running vcftidy on my VCF file:\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/ubuntu/software/vcftidy-master/vcftidy.py\", line 527, in <module>\r\n    sys.exit(main(fh, ref))\r\n  File \"/home/ubuntu/software/vcftidy-master/vcftidy.py\", line 495, in main\r\n    for v in gen_variants(fh):\r\n  File \"/home/ubuntu/software/vcftidy-master/vcftidy.py\", line 472, in gen_variants\r\n    fields[1], fields[3], fields[4] = leftnorm(fields[0], pos, ref, alts[0], fa)\r\n  File \"/home/ubuntu/software/vcftidy-master/vcftidy.py\", line 440, in leftnorm\r\n    return normalize(*leftalign(chrom, pos, ref, alt, fa), left_only=True)\r\n  File \"/home/ubuntu/software/vcftidy-master/vcftidy.py\", line 322, in leftalign\r\n    assert seq.endswith(ref), (chrom, pos, ref, alt, seq[-10:])\r\nAssertionError: ('chr1', 893981, 'C', 'T', u'ctcttcagcc')\r\n\r\nI do not get any errors using vt, but the docs mentioned that vcftidy is better to use.\r\n\r\nIs there a conflict between the call and the reference genome?  I used the same reference genome for both.\r\n\r\nHappy to provide more information.  I can send you the vcf file with that specific entry if you like.  Thanks in advance.  Great new update!\r\n\r\nGEMINI: 0.12.2\r\nOS: Ubuntu 14.04.2 LTS\r\n\r\nKind regards,\r\nNima Farzaneh"}}