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Please use 'VCF' instead.\\nYou can extract VCF fields to a TXT file using 'SnpSift extractFields' (http://snpeff.sourceforge.net/SnpSift.html#Extract).\");","path":"src/main/java/ca/mcgill/mcb/pcingola/snpEffect/commandLine/SnpEffCmdEff.java","position":70,"original_position":70,"commit_id":"67c36a5ec6b11b6c228dc9048805889410c49d80","original_commit_id":"67c36a5ec6b11b6c228dc9048805889410c49d80","user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"body":"Remove createSummary\r\nSet createSummaryHtml = true  (default)\r\nSet createSummaryCsv = false (default)\r\n","created_at":"2015-08-04T14:11:48Z","updated_at":"2015-08-04T14:11:48Z","html_url":"https://github.com/pcingola/SnpEff/pull/91#discussion_r36191671","pull_request_url":"https://api.github.com/repos/pcingola/SnpEff/pulls/91","_links":{"self":{"href":"https://api.github.com/repos/pcingola/SnpEff/pulls/comments/36191671"},"html":{"href":"https://github.com/pcingola/SnpEff/pull/91#discussion_r36191671"},"pull_request":{"href":"https://api.github.com/repos/pcingola/SnpEff/pulls/91"}}},"pull_request":{"url":"https://api.github.com/repos/pcingola/SnpEff/pulls/91","id":41508538,"html_url":"https://github.com/pcingola/SnpEff/pull/91","diff_url":"https://github.com/pcingola/SnpEff/pull/91.diff","patch_url":"https://github.com/pcingola/SnpEff/pull/91.patch","issue_url":"https://api.github.com/repos/pcingola/SnpEff/issues/91","number":91,"state":"open","locked":false,"title":"options to output both csv and html","user":{"login":"ExpressionAnalysis","id":13385925,"avatar_url":"https://avatars.githubusercontent.com/u/13385925?v=3","gravatar_id":"","url":"https://api.github.com/users/ExpressionAnalysis","html_url":"https://github.com/ExpressionAnalysis","followers_url":"https://api.github.com/users/ExpressionAnalysis/followers","following_url":"https://api.github.com/users/ExpressionAnalysis/following{/other_user}","gists_url":"https://api.github.com/users/ExpressionAnalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/ExpressionAnalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ExpressionAnalysis/subscriptions","organizations_url":"https://api.github.com/users/ExpressionAnalysis/orgs","repos_url":"https://api.github.com/users/ExpressionAnalysis/repos","events_url":"https://api.github.com/users/ExpressionAnalysis/events{/privacy}","received_events_url":"https://api.github.com/users/ExpressionAnalysis/received_events","type":"User","site_admin":false},"body":"We're interested in being able to output both csv and html formats for SnpEff.  So, I've introduced options to allow one or the other or both, i.e., -htmlStats and -csvStats. Example usage,\r\njava -jar snpEff.jar -c asnpeffconfigfile.config -o vcf -v -csvStats test.csv -htmlStats test.html GRCh37.75 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