{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/3734","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/3734/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/3734/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/3734/events","html_url":"https://github.com/broadinstitute/gatk/issues/3734","id":267722109,"number":3734,"title":"VCF header: FLOAT vs INTEGER causing issues","user":{"login":"chandrans","id":6998669,"avatar_url":"https://avatars2.githubusercontent.com/u/6998669?v=4","gravatar_id":"","url":"https://api.github.com/users/chandrans","html_url":"https://github.com/chandrans","followers_url":"https://api.github.com/users/chandrans/followers","following_url":"https://api.github.com/users/chandrans/following{/other_user}","gists_url":"https://api.github.com/users/chandrans/gists{/gist_id}","starred_url":"https://api.github.com/users/chandrans/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chandrans/subscriptions","organizations_url":"https://api.github.com/users/chandrans/orgs","repos_url":"https://api.github.com/users/chandrans/repos","events_url":"https://api.github.com/users/chandrans/events{/privacy}","received_events_url":"https://api.github.com/users/chandrans/received_events","type":"User","site_admin":false},"labels":[{"id":244151192,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/Vanilla","name":"Vanilla","color":"ededed","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-10-23T15:53:44Z","updated_at":"2017-10-25T18:38:41Z","closed_at":"2017-10-25T18:38:41Z","author_association":"CONTRIBUTOR","body":"It seems a lot of users use bcftools on their VCFs, and it sometimes converts floats to integers. For example MQ=31.0 to MQ=31. This change causes GATK tools to error. Is it possible to relax this validation?\n\n----\nUser Report\n----\n\nHi,\n\nEvery time I had this message, this was due to bcftools which can change some float values to an integer representation : (e.g : before bcftools : MQ=31.0; after bcftools : MQ=31). \n\nThe fact that GATK is very strict on that subject (40.0 is considered as a float while 40 is not) have some advantages and some drawbacks. I hope this problem will be resolved in GATK4 because bcftools is really useful and widely used when dealing with vcf files.\n\nThis Issue was generated from your [forums] \n[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/43270#Comment_43270\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/339429233","html_url":"https://github.com/broadinstitute/gatk/issues/3734#issuecomment-339429233","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/3734","id":339429233,"user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars3.githubusercontent.com/u/4700332?v=4","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"created_at":"2017-10-25T18:38:41Z","updated_at":"2017-10-25T18:38:41Z","author_association":"COLLABORATOR","body":"@chandrans I briefly looked into this, and it looks like this is likely a problem with the gatk3 implementation of median which is very brittle to type issues.  I don't think gatk4 suffers from this problem.  It's up to @vdauwera I guess if we want to fix it in gatk3, but I'm going to close the issue here.  Feel free to reopen if someone encounters it in gatk4.  I suspect that changing the header may not fix the problem in gatk3, it's more likely that it's an issue with the htsjdk parsing that assumes anything that doesn't have a `.` should be treated as an int, while neighboring values are treated as doubles.  "}}
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