{"action":"created","issue":{"url":"https://api.github.com/repos/etal/cnvkit/issues/7","labels_url":"https://api.github.com/repos/etal/cnvkit/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/etal/cnvkit/issues/7/comments","events_url":"https://api.github.com/repos/etal/cnvkit/issues/7/events","html_url":"https://github.com/etal/cnvkit/issues/7","id":60431601,"number":7,"title":"LOH: Read germline SNPs from paired tumor-normal VCF","user":{"login":"etal","id":52723,"avatar_url":"https://avatars.githubusercontent.com/u/52723?v=3","gravatar_id":"","url":"https://api.github.com/users/etal","html_url":"https://github.com/etal","followers_url":"https://api.github.com/users/etal/followers","following_url":"https://api.github.com/users/etal/following{/other_user}","gists_url":"https://api.github.com/users/etal/gists{/gist_id}","starred_url":"https://api.github.com/users/etal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/etal/subscriptions","organizations_url":"https://api.github.com/users/etal/orgs","repos_url":"https://api.github.com/users/etal/repos","events_url":"https://api.github.com/users/etal/events{/privacy}","received_events_url":"https://api.github.com/users/etal/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-10T00:14:09Z","updated_at":"2015-05-14T01:22:47Z","closed_at":null,"body":"The functions to plot loss-of-heterozygosity (LOH) take allele frequencies from a given VCF file. LOH is only visible in germline SNPs that are also present in the tumor sample. Currently, all SNVs in the VCF are plotted, so this works best if the user had the foresight to separately filter the tumor variants for germline SNPs first.\r\n\r\nVCFs from MuTect, FreeBayes and other variant callers will list the SNPs/SNVs in a matched tumor-normal pair together; this makes it feasible for CNVkit to parse this VCF and extract only the allele frequencies of SNPs for plotting.\r\n\r\nThe tumor sample name can be specified with `-i` now. *Next:*\r\n- Add `-n` to specify the normal sample name in the same VCF.\r\n- If `-n` is unspecified and there are 2 or more samples, look for \"NORMAL\" (case-insensitive); if `-i`is unspecified, look for \"TUMOR\".\r\n- Fall back to current behavior if none of this magic works."},"comment":{"url":"https://api.github.com/repos/etal/cnvkit/issues/comments/101874838","html_url":"https://github.com/etal/cnvkit/issues/7#issuecomment-101874838","issue_url":"https://api.github.com/repos/etal/cnvkit/issues/7","id":101874838,"user":{"login":"etal","id":52723,"avatar_url":"https://avatars.githubusercontent.com/u/52723?v=3","gravatar_id":"","url":"https://api.github.com/users/etal","html_url":"https://github.com/etal","followers_url":"https://api.github.com/users/etal/followers","following_url":"https://api.github.com/users/etal/following{/other_user}","gists_url":"https://api.github.com/users/etal/gists{/gist_id}","starred_url":"https://api.github.com/users/etal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/etal/subscriptions","organizations_url":"https://api.github.com/users/etal/orgs","repos_url":"https://api.github.com/users/etal/repos","events_url":"https://api.github.com/users/etal/events{/privacy}","received_events_url":"https://api.github.com/users/etal/received_events","type":"User","site_admin":false},"created_at":"2015-05-14T01:22:47Z","updated_at":"2015-05-14T01:22:47Z","body":"With 9730f89, we're mostly there. Remaining work:\r\n\r\n1. In the FreeBayes and MuTect files I'm working with, the SNPs we need for this plot are marked \"REJECT\" in the FILTER column, so I've added an option to keep these lines by default, which I suspect might break something in bcbio-nextgen (holla @chapmanb @roryk) -- any suggestions for a better method would be greatly appreciated.\r\n\r\n2. For tumor-only VCFs, or paired T/N VCFs with lingering noise, it would be nice to take another VCF of known SNPs from 1000 Genomes, dbSNP 129, ESP 6500, etc. and further filter the variants in the given sample.\r\n\r\n3. @Lenbok - Which callers add the PEDIGREE line? I'll add a check for it if I can do so reliably."}}