{"action":"opened","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/651","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/651/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/651/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/651/events","html_url":"https://github.com/samtools/bcftools/issues/651","id":244183598,"number":651,"title":"bcftools annotate provides cryptic error message","user":{"login":"freeseek","id":1829330,"avatar_url":"https://avatars1.githubusercontent.com/u/1829330?v=4","gravatar_id":"","url":"https://api.github.com/users/freeseek","html_url":"https://github.com/freeseek","followers_url":"https://api.github.com/users/freeseek/followers","following_url":"https://api.github.com/users/freeseek/following{/other_user}","gists_url":"https://api.github.com/users/freeseek/gists{/gist_id}","starred_url":"https://api.github.com/users/freeseek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/freeseek/subscriptions","organizations_url":"https://api.github.com/users/freeseek/orgs","repos_url":"https://api.github.com/users/freeseek/repos","events_url":"https://api.github.com/users/freeseek/events{/privacy}","received_events_url":"https://api.github.com/users/freeseek/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-07-19T21:44:30Z","updated_at":"2017-07-19T21:44:30Z","closed_at":null,"body":"I am trying to annotate a VCF file using a TSV file, but I am getting no luck. Here is code to reproduce the issue:\r\n\r\nGenerating an annotation TSV file:\r\n`echo -e \"20\\t60810\\t0.527888\" | bgzip > annot.tsv.gz && tabix -fb2 annot.tsv.gz`\r\n\r\nPiping a VCF file for a variant to be annotated:\r\n```\r\n(echo \"##fileformat=VCFv4.1\"\r\necho \"##contig=<ID=20,length=63025520>\"\r\necho -e \"#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\"\r\necho -e \"20\\t60810\\t.\\tT\\tG\\t.\\t.\\t.\") |\r\n  bcftools annotate --no-version -a annot.tsv.gz -c CHROM,POS,GC \\\r\n  -h <(echo \"##INFO=<ID=GC,Number=1,Type=Float,Description=\\\"GC content around the variant\\\">\")\r\n```\r\n\r\nThis is the outcome I get:\r\n```\r\n[E::bcf_sr_regions_next] Could not parse the file annot.tsv.gz, using the columns 1,2,5\r\n##fileformat=VCFv4.1\r\n##FILTER=<ID=PASS,Description=\"All filters passed\">\r\n##contig=<ID=20,length=63025520>\r\n##INFO=<ID=GC,Number=1,Type=Float,Description=\"GC content around the variant\">\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO\r\n20      60810   .       T       G       .       .       .\r\n```\r\nWith the variant not annotated and a cryptic error (i.e. why is it referring to non-existing column 5?).\r\n\r\nI cannot understand what I am doing wrong. The documentation is very unclear. Would it be possible to have a few example to show how this is supposed to work (see `https://samtools.github.io/bcftools/bcftools.html`)?"}}
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