{"action":"opened","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/346","repository_url":"https://api.github.com/repos/galaxyproject/tools-devteam","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/346/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/346/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/346/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/346","id":140693724,"number":346,"title":"Where is Samtools view? ","user":{"login":"zfrenchee","id":2761597,"avatar_url":"https://avatars.githubusercontent.com/u/2761597?v=3","gravatar_id":"","url":"https://api.github.com/users/zfrenchee","html_url":"https://github.com/zfrenchee","followers_url":"https://api.github.com/users/zfrenchee/followers","following_url":"https://api.github.com/users/zfrenchee/following{/other_user}","gists_url":"https://api.github.com/users/zfrenchee/gists{/gist_id}","starred_url":"https://api.github.com/users/zfrenchee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zfrenchee/subscriptions","organizations_url":"https://api.github.com/users/zfrenchee/orgs","repos_url":"https://api.github.com/users/zfrenchee/repos","events_url":"https://api.github.com/users/zfrenchee/events{/privacy}","received_events_url":"https://api.github.com/users/zfrenchee/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-14T14:43:07Z","updated_at":"2016-03-14T14:43:07Z","closed_at":null,"body":"Hello, \r\nAnother naive question, but I'm trying to filter out mitochondrial reads from a bam file on galaxy. Right now I'm essentially mimicking [this approach](https://www.biostars.org/p/128967/) with \r\n\r\n`samtools idxstats input.bam | cut -f 1 | grep -v MT | xargs samtools view -b input.bam > output.bam`\r\n\r\nexcept the last step requires `samtools view -b`. I'm thinking there's either a blindingly obvious way to do this or there's just a better way to filter out mitochondrial reads on galaxy. Hints in either of those directions would be super helpful!"}}