{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/comments/43323682","id":43323682,"diff_hunk":"@@ -144,3 +147,329 @@ Otherwise you will need to tell the VM each time as well like so:\n ```\n java -Djava.library.path=wherever-i-downloaded-the-jnilib -jar hellbender-protected.jar ...\n ```\n+\n+The CNV case and PoN workflows (description and examples)\n+---------------------------------------------------------\n+\n+#### Requirements\n+1. Java 1.8\n+2. A functioning GATK4-protected jar (hellbender-protected.jar)\n+3. HDF5 1.8.13 \n+4. The location of the HDF5-Java JNI Libraries Release 2.9 (2.11 for Macs).  (See platform instructions above for typical locations)  \n+5. Reference genome (fasta) with fai and dict indexes.  This can be downloaded as part of the GATK resource bundle: http://www.broadinstitute.org/gatk/guide/article?id=1213\n+6. target BED file that was used to create the PoN file.  Format details can be found `here <http://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_ .  **NOTE:**  For the CNV tools, you will need a fourth column for target name, which must be unique across rows.\n+```\n+1       12200   12275   target1\n+1       13505   13600   target2\n+1       31000   31500   target3\n+1       35138   35174   target4\n+....snip....\n+```\n+7. PoN file (when running case samples only).  This file should be created using the Create PoN workflow (see below).\n+8. Sample name (when running case samples only).  This can be extracted from the input bam file by looking at the ``SM`` tag.  Use ``samtools view -H my_sample.bam | egrep SM``.\n+\n+#### Case sample workflow\n+\n+This workflow requires a PoN file generated by the Create PoN workflow.\n+\n+If you do not have a PoN, please skip to the [Create PoN workflow](#create-pon-workflow), below ....\n+\n+##### Overview of steps\n+\n+- Step 1. Collect proportional coverage\n+- Step 2. Create coverage profile\n+- Step 3. Segment coverage profile\n+- Step 4. Call segments\n+\n+##### Step 1. Collect proportional coverage\n+\n+###### Inputs\n+- bam file\n+- target bed file -- must be the same that was used for the PoN\n+- reference_sequence (required by GATK) -- fasta file with hg19 reference.  ","path":"README.md","position":122,"original_position":122,"commit_id":"a52b286c462bef0c3882ba78eb23501d5b0dc67d","original_commit_id":"a52b286c462bef0c3882ba78eb23501d5b0dc67d","user":{"login":"vdauwera","id":2748435,"avatar_url":"https://avatars.githubusercontent.com/u/2748435?v=3","gravatar_id":"","url":"https://api.github.com/users/vdauwera","html_url":"https://github.com/vdauwera","followers_url":"https://api.github.com/users/vdauwera/followers","following_url":"https://api.github.com/users/vdauwera/following{/other_user}","gists_url":"https://api.github.com/users/vdauwera/gists{/gist_id}","starred_url":"https://api.github.com/users/vdauwera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vdauwera/subscriptions","organizations_url":"https://api.github.com/users/vdauwera/orgs","repos_url":"https://api.github.com/users/vdauwera/repos","events_url":"https://api.github.com/users/vdauwera/events{/privacy}","received_events_url":"https://api.github.com/users/vdauwera/received_events","type":"User","site_admin":false},"body":"When you say hg19, do you mean real hg19 (with contigs chr1 etc) or the Cancer group's version of hg19, which is really b37 under the hood?\r\n\r\nOy. Reading down to the Outputs section I can see it's b37. And I'm assuming any resources provided follow in the grand old tradition of being called hg19 but following the b37 naming conventions.  \r\n\r\nGuys, this needs to be sorted out clearly as it's a huge point of pain for the community. I know that as far as the cancer group is concerned everything is internally consistent, but this is going to collide big time with the GATK resource bundle and so on. People are going to have a hell of a time with dictionary mismatches and so on. We need to find a way to deal with this sanely. I don't suppose we can just rename everything to b37? ","created_at":"2015-10-28T21:53:31Z","updated_at":"2015-10-28T21:53:31Z","html_url":"https://github.com/broadinstitute/hellbender-protected/pull/167#discussion_r43323682","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/167","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/comments/43323682"},"html":{"href":"https://github.com/broadinstitute/hellbender-protected/pull/167#discussion_r43323682"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/167"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/pulls/167","id":48953568,"html_url":"https://github.com/broadinstitute/hellbender-protected/pull/167","diff_url":"https://github.com/broadinstitute/hellbender-protected/pull/167.diff","patch_url":"https://github.com/broadinstitute/hellbender-protected/pull/167.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/167","number":167,"state":"open","locked":false,"title":"Updating docs based on conversation with Geraldine.","user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"body":"Updating link\r\n\r\nTesting link\r\n\r\nFinished the create PoN workflow description/examples\r\n\r\nFixed formatting issue.\r\n\r\nFixed formatting issue.\r\n\r\nFixed missing data in example\r\n\r\nCloses #150 \r\n\r\n@vdauwera Feel free to review as well.\r\n\r\n@davidbenjamin You may want to view it in the issue150 branch.  That way it renders nicely.","created_at":"2015-10-28T01:08:17Z","updated_at":"2015-10-28T21:53:31Z","closed_at":null,"merged_at":null,"merge_commit_sha":"4a53056f6cb96920cf16505eb57b5fd5bbe145f5","assignee":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/milestones/3","html_url":"https://github.com/broadinstitute/hellbender-protected/milestones/CNV%20Tools%20(ReCapSeg%20only)%20alpha%20release","labels_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/milestones/3/labels","id":1222082,"number":3,"title":"CNV Tools (ReCapSeg only) alpha release","description":"This will be the alpha release of CNV tools.  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