{"action":"created","issue":{"url":"https://api.github.com/repos/andyrimmer/Platypus/issues/61","repository_url":"https://api.github.com/repos/andyrimmer/Platypus","labels_url":"https://api.github.com/repos/andyrimmer/Platypus/issues/61/labels{/name}","comments_url":"https://api.github.com/repos/andyrimmer/Platypus/issues/61/comments","events_url":"https://api.github.com/repos/andyrimmer/Platypus/issues/61/events","html_url":"https://github.com/andyrimmer/Platypus/issues/61","id":207208767,"number":61,"title":"Interpretation of FORMAT/NR and FORMAT/NV for multiallelic sites","user":{"login":"holtgrewe","id":521780,"avatar_url":"https://avatars3.githubusercontent.com/u/521780?v=3","gravatar_id":"","url":"https://api.github.com/users/holtgrewe","html_url":"https://github.com/holtgrewe","followers_url":"https://api.github.com/users/holtgrewe/followers","following_url":"https://api.github.com/users/holtgrewe/following{/other_user}","gists_url":"https://api.github.com/users/holtgrewe/gists{/gist_id}","starred_url":"https://api.github.com/users/holtgrewe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/holtgrewe/subscriptions","organizations_url":"https://api.github.com/users/holtgrewe/orgs","repos_url":"https://api.github.com/users/holtgrewe/repos","events_url":"https://api.github.com/users/holtgrewe/events{/privacy}","received_events_url":"https://api.github.com/users/holtgrewe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-02-13T12:45:49Z","updated_at":"2017-06-21T07:17:28Z","closed_at":null,"body":"Dear Andy,\r\n\r\nHow do I interpret the NR and NV fields in the presence of multi-allelic alleles?\r\n\r\nConsider the following line, for example.\r\n\r\nhs37d5\t35158918\t.\tTGCGGC\tCGCGGC,CGCGGT\t1553\tPASS\tFR=0.25,0.25;MMLQ=33.0;TCR=357;HP=1;WE=35158931;Source=Platypus;WS=35158881;PP=1090.0,1553.0;TR=241,117;NF=88,46;TCF=230;NR=153,71;TC=587;MGOF=40;SbPval=0.56;MQ=58.9;QD=4.667100467;SC=GCCCTGGAGATGCGGCCCCCA;BRF=0.1;HapScore=3\tGT:GL:GOF:GQ:NR:NV\t1/0:-1.0,-1.0,-1.0:35.0:99:235,235:99,34\t2/0:-1.0,-1.0,-1.0:29.0:99:89,89:35,33\t2/0:-1.0,-1.0,-1.0:37.0:99:183,183:73,33\t1/0:-1.0,-1.0,-1.0:40.0:99:80,80:34,17\r\n\r\nWhat is given here?\r\n"},"comment":{"url":"https://api.github.com/repos/andyrimmer/Platypus/issues/comments/309985327","html_url":"https://github.com/andyrimmer/Platypus/issues/61#issuecomment-309985327","issue_url":"https://api.github.com/repos/andyrimmer/Platypus/issues/61","id":309985327,"user":{"login":"baraaorabi","id":6283321,"avatar_url":"https://avatars3.githubusercontent.com/u/6283321?v=3","gravatar_id":"","url":"https://api.github.com/users/baraaorabi","html_url":"https://github.com/baraaorabi","followers_url":"https://api.github.com/users/baraaorabi/followers","following_url":"https://api.github.com/users/baraaorabi/following{/other_user}","gists_url":"https://api.github.com/users/baraaorabi/gists{/gist_id}","starred_url":"https://api.github.com/users/baraaorabi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/baraaorabi/subscriptions","organizations_url":"https://api.github.com/users/baraaorabi/orgs","repos_url":"https://api.github.com/users/baraaorabi/repos","events_url":"https://api.github.com/users/baraaorabi/events{/privacy}","received_events_url":"https://api.github.com/users/baraaorabi/received_events","type":"User","site_admin":false},"created_at":"2017-06-21T07:17:28Z","updated_at":"2017-06-21T07:17:28Z","body":"Hey Andy,\r\n\r\nI ran Platypus with a single sample, and I got this multi-allelic variant record:\r\n\r\n`16\t3294154\t.\tGTT\tG,GT\t1188\tbadReads;QD\tBRF=0.73;FR=0.5000,0.5000;HP=11;HapScore=2;MGOF=17;MMLQ=38;MQ=60.0;NF=0,0;NR=129,129;PP=695,1188;QD=5.45736434109;SC=CAGGTGTTTGGTTTTTTTTTT;SbPval=1.0;Source=Platypus;TC=135;TCF=0;TCR=135;TR=129,129;WE=3294164;WS=3294144\tGT:GL:GOF:GQ:NR:NV\t1/2:-1,-1,-1:17:99:135,135:129,129\r\n`\r\n\r\nI am confused by NV and NR numbers from FORMAT field here. In INFO field, TC (\"Total coverage at this locus\") is 135. If as you are saying in this thread, NR of FORMAT is \"number of reads supporting the reference\", wouldn't this mean that all reads (aka TC) are reads supporting the reference?\r\n\r\nAdditionally, is the case of this VCF record a case in which all 129 reads support both variants simultaneously? Is there an arithmetic way that I can separate reads into two separate variants directly from the VCF file?\r\n\r\nThanks a ton!\r\n"}}
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