{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1316","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1316/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1316/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1316/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1316","id":146556321,"number":1316,"title":"Problem with Samtools and coverage computations ","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-04-07T09:12:58Z","updated_at":"2016-04-07T12:18:00Z","closed_at":null,"body":"I am running `bcbio.variation.coverage` computations on a WGS sample with a region BED file that contains all human genes. My intention is to get the coverage report for my priority regions (which happen to be all genes) with annotation of difficult regions. In the `priority_coverage` function of that module, in line `311`, `samtools` is called with the coordinates of all regions in the command line call. That fails with a broken pipe error from samtools, probably because the commend line gets too long (it seems to contain all regions of at least one chromosome). `samtools` also allows specifying these regions by a BED file using the `-L` command. Would that be a more robust option?"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/206847068","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1316#issuecomment-206847068","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1316","id":206847068,"user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"created_at":"2016-04-07T12:18:00Z","updated_at":"2016-04-07T12:18:00Z","body":"Got it, it's the changed bedtools syntax. Bcbio installed bedtools 2.24.0, and there the syntax should be `-b BEDFILE -abam stdin` instead of `-a BEDFILE -b -`. In the bedtools documentation it says that the syntax changed from 2.24.0 on. "}}