{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/hts-specs/issues/77","labels_url":"https://api.github.com/repos/samtools/hts-specs/issues/77/labels{/name}","comments_url":"https://api.github.com/repos/samtools/hts-specs/issues/77/comments","events_url":"https://api.github.com/repos/samtools/hts-specs/issues/77/events","html_url":"https://github.com/samtools/hts-specs/issues/77","id":64490738,"number":77,"title":"How to represent reference allele in gt calls when splitting multiple alternative alleles","user":{"login":"moonso","id":405278,"avatar_url":"https://avatars.githubusercontent.com/u/405278?v=3","gravatar_id":"","url":"https://api.github.com/users/moonso","html_url":"https://github.com/moonso","followers_url":"https://api.github.com/users/moonso/followers","following_url":"https://api.github.com/users/moonso/following{/other_user}","gists_url":"https://api.github.com/users/moonso/gists{/gist_id}","starred_url":"https://api.github.com/users/moonso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/moonso/subscriptions","organizations_url":"https://api.github.com/users/moonso/orgs","repos_url":"https://api.github.com/users/moonso/repos","events_url":"https://api.github.com/users/moonso/events{/privacy}","received_events_url":"https://api.github.com/users/moonso/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-03-26T10:27:55Z","updated_at":"2015-03-27T15:41:59Z","closed_at":null,"body":"There are many of us who are splitting multiallelic calls in the vcf for downstream annotation etc.\r\nOne if the problem that arises is how to represent the new GT calls.\r\nExample:\r\n```\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  father  mother  proband\r\n3       947379  .       A       T,C     100     PASS    MQ=1    GT:GQ:AD:DP     1/1:60:0,7,0:12 0/2:60:7,0,10:17        1/2:60:0,7,8:16\r\n```\r\nIn a splitted version we could see:\r\n\r\n```\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  father  mother  proband\r\n3\t947379\t.\tA\tT\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\t1/1:60:0,7:12\t0/0:60:7,0:17\t0/1:60:0,7:16\r\n3\t947379\t.\tA\tC\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\t0/0:60:0,0:12\t0/1:60:7,10:17\t0/1:60:0,8:16\r\n```\r\nor perhaps:\r\n\r\n```\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  father  mother  proband\r\n3\t947379\t.\tA\tT\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\t1/1:60:0,7:12\t0/.:60:7,0:17\t./1:60:0,7:16\r\n3\t947379\t.\tA\tC\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\t./.:60:0,0:12\t0/1:60:7,10:17\t./1:60:0,8:16\r\n```\r\nBoth of these attempts are not accurate. \r\nIn the first example we say that we have seen the reference allele where we haven't.\r\nIn the second example we say that we do not know about the reference allele, even though we do know the exact genotype call.\r\nOne proposal would be to replace the '.' with another symbol to indicate that we are looking at a multiallelic position, maybe 'M' or something.\r\nThat would be:\r\n\r\n```\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  father  mother  proband\r\n3\t947379\t.\tA\tT\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\t1/1:60:0,7:12\t0/M:60:7,0:17\tM/1:60:0,7:16\r\n3\t947379\t.\tA\tC\t100\tPASS\tMQ=1\tGT:GQ:AD:DP\tM/M:60:0,0:12\t0/1:60:7,10:17\tM/1:60:0,8:16\r\n```\r\n\r\nAny thoughts or suggestions on this one?\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/hts-specs/issues/comments/86979602","html_url":"https://github.com/samtools/hts-specs/issues/77#issuecomment-86979602","issue_url":"https://api.github.com/repos/samtools/hts-specs/issues/77","id":86979602,"user":{"login":"lh3","id":480346,"avatar_url":"https://avatars.githubusercontent.com/u/480346?v=3","gravatar_id":"","url":"https://api.github.com/users/lh3","html_url":"https://github.com/lh3","followers_url":"https://api.github.com/users/lh3/followers","following_url":"https://api.github.com/users/lh3/following{/other_user}","gists_url":"https://api.github.com/users/lh3/gists{/gist_id}","starred_url":"https://api.github.com/users/lh3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lh3/subscriptions","organizations_url":"https://api.github.com/users/lh3/orgs","repos_url":"https://api.github.com/users/lh3/repos","events_url":"https://api.github.com/users/lh3/events{/privacy}","received_events_url":"https://api.github.com/users/lh3/received_events","type":"User","site_admin":false},"created_at":"2015-03-27T15:41:59Z","updated_at":"2015-03-27T15:41:59Z","body":"An unobserved allele could mean an allele known to be missing (@atks' case), or an allele that is possibly unobserved from data (SNP callers usually need to deal with this second case; old bcftools had been using allele \"X\" for years). I thought Broad and Sanger have reached a consensus on how to represent the second case, but I could not find it in the spec. Maybe it has not been settled yet.\r\n\r\nThe advantage of my proposal is that you can get the genotype from a single VCF line. The downside is we have to use a bunch of new INFO tags to annotate the first ALT allele only."}}