{"action":"opened","issue":{"url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/issues/168","repository_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts","labels_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/issues/168/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/issues/168/comments","events_url":"https://api.github.com/repos/BD2KGenomics/toil-scripts/issues/168/events","html_url":"https://github.com/BD2KGenomics/toil-scripts/issues/168","id":140407964,"number":168,"title":"Add adapter trimming to pipeline","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-12T19:01:44Z","updated_at":"2016-03-12T19:01:44Z","closed_at":null,"body":"There's a bit of confusion from the Harvard email thread as to whether the RAW BAMs have had their adapters trimmed or not. If you look at the hs37d5 BAMs, there are a fair number of hard clipped reads (but these all seem to be supplemental alignments). I'm going to add this to the pipeline (it's baked into BWAKIT, IIRC, so it's a simple add) and I think we should run a sample through with the adapter trimming just to sanity check."}}