{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/166","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/166/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/166/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/166/events","html_url":"https://github.com/broadinstitute/picard/issues/166","id":60818141,"number":166,"title":"MarkDuplicates question","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},"labels":[{"url":"https://api.github.com/repos/broadinstitute/picard/labels/question","name":"question","color":"cc317c"},{"url":"https://api.github.com/repos/broadinstitute/picard/labels/user","name":"user","color":"009800"},{"url":"https://api.github.com/repos/broadinstitute/picard/labels/Vanilla","name":"Vanilla","color":"ededed"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-03-12T13:27:20Z","updated_at":"2015-03-12T22:43:58Z","closed_at":"2015-03-12T17:37:28Z","body":"User is confused about exactly what criteria are used by MarkDuplicates. GATK docs say it marks as dupes reads that have the same start pos and identical CIGAR, but it looks like Picard docs say nothing about CIGAR, and just mentions length. We need to reconcile this (I expect the GATK doc needs to be corrected). \n\nSecondary question is how it chooses which read is kept as non-dupe -- random or highest MAPQ? \n\n\nThis Issue was generated from your [forums] \n[forums]: http://gatkforums.broadinstitute.org/discussion/5227/markduplicates/p1\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/78669109","html_url":"https://github.com/broadinstitute/picard/issues/166#issuecomment-78669109","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/166","id":78669109,"user":{"login":"amilev","id":2745839,"avatar_url":"https://avatars.githubusercontent.com/u/2745839?v=3","gravatar_id":"","url":"https://api.github.com/users/amilev","html_url":"https://github.com/amilev","followers_url":"https://api.github.com/users/amilev/followers","following_url":"https://api.github.com/users/amilev/following{/other_user}","gists_url":"https://api.github.com/users/amilev/gists{/gist_id}","starred_url":"https://api.github.com/users/amilev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amilev/subscriptions","organizations_url":"https://api.github.com/users/amilev/orgs","repos_url":"https://api.github.com/users/amilev/repos","events_url":"https://api.github.com/users/amilev/events{/privacy}","received_events_url":"https://api.github.com/users/amilev/received_events","type":"User","site_admin":false},"created_at":"2015-03-12T22:43:58Z","updated_at":"2015-03-12T22:43:58Z","body":"Do you know if it work also with the RNA N's?\nOn Mar 12, 2015 1:36 PM, \"Geraldine Van der Auwera\" <\nnotifications@github.com> wrote:\n\n> Indeed, thanks Tim.\n>\n> From the FAQ:\n>\n> Q: How does MarkDuplicates work?\n>\n> A: Essentially what it does (for pairs; single-end data is also handled) is\n> to find the 5' coordinates and mapping orientations of each read pair. When\n> doing this it takes into account all clipping that has taking place as well\n> as any gaps or jumps in the alignment. You can thus think of it as\n> determining \"if all the bases from the read were aligned, where would the\n> 5' most base have been aligned\". It then matches all read pairs that have\n> identical 5' coordinates and orientations and marks as duplicates all but\n> the \"best\" pair. \"Best\" is defined as the read pair having the highest sum\n> of base qualities as bases with Q >= 15.\n>\n> If your reads have been divided into separate BAMs by chromosome,\n> inter-chromosomal pairs will not be identified, but MarkDuplicates will not\n> fail due to inability to find the mate pair for a read.\n>\n> On Thu, Mar 12, 2015 at 12:25 PM, Tim Fennell <notifications@github.com>\n> wrote:\n>\n> > FYI most of this is covered in the picard FAQ:\n> >\n> > http://broadinstitute.github.io/picard/faq.html <\n> > http://broadinstitute.github.io/picard/faq.html>\n> >\n> > -t\n> >\n> > > On Mar 12, 2015, at 10:44 AM, Nils Homer <notifications@github.com>\n> > wrote:\n> > >\n> > > @vdauwera <https://github.com/vdauwera> we should write this up, as it\n> > is not what is in the GATK doc and not what you describe above. This\n> would\n> > be a great thing to document correctly.\n> > >\n> > > @splaisan <https://github.com/splaisan> you can look at the admittedly\n> > complex code in the markduplicates subdirectories:\n> >\n> https://github.com/broadinstitute/picard/tree/master/src/java/picard/sam/markduplicates\n> > <\n> >\n> https://github.com/broadinstitute/picard/tree/master/src/java/picard/sam/markduplicates\n> > >\n> > > No such user tool exists.\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub <\n> >\n> https://github.com/broadinstitute/picard/issues/166#issuecomment-78493299\n> > >.\n> >\n> > >\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <\n> https://github.com/broadinstitute/picard/issues/166#issuecomment-78516925>\n> > .\n> >\n>\n>\n>\n> --\n> Geraldine A. Van der Auwera, Ph.D.\n> Bioinformatics Scientist II\n> GATK Support & Outreach\n> Broad Institute\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/broadinstitute/picard/issues/166#issuecomment-78540865>\n> .\n>\n"}}