{"action":"created","issue":{"url":"https://api.github.com/repos/ANGSD/angsd/issues/18","labels_url":"https://api.github.com/repos/ANGSD/angsd/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/ANGSD/angsd/issues/18/comments","events_url":"https://api.github.com/repos/ANGSD/angsd/issues/18/events","html_url":"https://github.com/ANGSD/angsd/issues/18","id":107619932,"number":18,"title":"GL fields in output VCF don't sum to 1","user":{"login":"atcg","id":2090981,"avatar_url":"https://avatars.githubusercontent.com/u/2090981?v=3","gravatar_id":"","url":"https://api.github.com/users/atcg","html_url":"https://github.com/atcg","followers_url":"https://api.github.com/users/atcg/followers","following_url":"https://api.github.com/users/atcg/following{/other_user}","gists_url":"https://api.github.com/users/atcg/gists{/gist_id}","starred_url":"https://api.github.com/users/atcg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/atcg/subscriptions","organizations_url":"https://api.github.com/users/atcg/orgs","repos_url":"https://api.github.com/users/atcg/repos","events_url":"https://api.github.com/users/atcg/events{/privacy}","received_events_url":"https://api.github.com/users/atcg/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-09-21T23:47:39Z","updated_at":"2015-10-12T17:19:35Z","closed_at":"2015-10-12T17:19:35Z","body":"Hello,\r\nI've been trying to output a VCF file to look at IBD between samples, and I was curious if the GL's in the VCF file are scaled in any way. It says they have been scaled to add up to 1 in the header of the VCF, but they don't (the GP fields do sum to 1).\r\n\r\nHere's the command I used:\r\nangsd0.902/angsd -bam bamlist.txt -out OUTPUT -uniqueOnly 1 -only_proper_pairs 1 -remove_bads 1 -doCounts 1 -nThreads 27 -doMaf 1 -doMajorMinor 2 -GL 2 -minMapQ 20 -minQ 30 -dovcf 1 -doPost 2\r\n\r\nAnd here's what my VCF looks like:\r\n\r\n##fileformat=VCFv4.2(angsd version)\r\n##FORMAT=\\<ID=GT,Number=1,Type=Integer,Description=\"Genotype\"\\>\r\n##FORMAT=\\<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\"\\>\r\n##FORMAT=\\<ID=PL,Number=G,Type=Float,Description=\"Phred-scaled Genotype Likelihoods\"\\>\r\n##FORMAT=\\<ID=GL,Number=G,Type=Float,Description=\"scaled Genotype Likelihoods (these are really llh eventhough they sum to one)\"\\>\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ind0    ind1\r\nscaffold_0      1616    .       T       A       .       PASS    .       GP:GL   0.666631,0.333333,0.000035:0.000000,-0.301007,-4.277052 0.666578,0.333333,0.000088:0.000000,-0.300972,-3.876948\r\n\r\nThanks very much for any insight!\r\nEvan"},"comment":{"url":"https://api.github.com/repos/ANGSD/angsd/issues/comments/147466740","html_url":"https://github.com/ANGSD/angsd/issues/18#issuecomment-147466740","issue_url":"https://api.github.com/repos/ANGSD/angsd/issues/18","id":147466740,"user":{"login":"ANGSD","id":6351086,"avatar_url":"https://avatars.githubusercontent.com/u/6351086?v=3","gravatar_id":"","url":"https://api.github.com/users/ANGSD","html_url":"https://github.com/ANGSD","followers_url":"https://api.github.com/users/ANGSD/followers","following_url":"https://api.github.com/users/ANGSD/following{/other_user}","gists_url":"https://api.github.com/users/ANGSD/gists{/gist_id}","starred_url":"https://api.github.com/users/ANGSD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ANGSD/subscriptions","organizations_url":"https://api.github.com/users/ANGSD/orgs","repos_url":"https://api.github.com/users/ANGSD/repos","events_url":"https://api.github.com/users/ANGSD/events{/privacy}","received_events_url":"https://api.github.com/users/ANGSD/received_events","type":"User","site_admin":false},"created_at":"2015-10-12T17:19:35Z","updated_at":"2015-10-12T17:19:35Z","body":"Ok, I'm closing this issue. Feel free to reopen if needed"}}