{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1662","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1662/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1662/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1662/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1662","id":192508087,"number":1662,"title":"Variant calling not parallelized by split regions in WGS analysis","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,"assignees":[],"milestone":null,"comments":7,"created_at":"2016-11-30T08:52:00Z","updated_at":"2016-11-30T14:09:58Z","closed_at":null,"body":"I am running a 100-sample WGS batch with the `variant2` workflow and \r\n\r\n```\r\nnomap_split_size: 250\r\nnomap_split_targets: 200\r\nvariantcaller: vardict\r\n```\r\n\r\nI would expect that variant calling is parallelized also within a single sample by using the split regions (split at unmapped/N reference); however, that is not the case in my current run. Instead, the `vardict-java` pipe is applied on each full chromosome rather than on the mapped blocks in each chromosome. Is there any advice on how I can find out why that may be the case? \r\n\r\nObviously, that limits scalability quiet a lot for me (especially since the limiting step in the `vardict` pipe is an R script, `teststrandbias.R`, which seems to take forever) and I was under the impression that parallelization by subregions still worked in my last largish WGS analysis 2 months ago. Thanks!"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/263882141","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1662#issuecomment-263882141","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1662","id":263882141,"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":"2016-11-30T14:09:58Z","updated_at":"2016-11-30T14:09:58Z","body":"@NeillGibson, I'd rather guess that this issue may have resulted from the `goleft` or Coverage QC integration earlier this month, but I'm not sure enough to blame a specific commit."}}
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