{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15","repository_url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation","labels_url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15/comments","events_url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15/events","html_url":"https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15","id":361646580,"node_id":"MDU6SXNzdWUzNjE2NDY1ODA=","number":15,"title":"SNPbam2vcf.py, line 247, KeyError: 'RG'","user":{"login":"mcetincompbio","id":42540331,"node_id":"MDQ6VXNlcjQyNTQwMzMx","avatar_url":"https://avatars1.githubusercontent.com/u/42540331?v=4","gravatar_id":"","url":"https://api.github.com/users/mcetincompbio","html_url":"https://github.com/mcetincompbio","followers_url":"https://api.github.com/users/mcetincompbio/followers","following_url":"https://api.github.com/users/mcetincompbio/following{/other_user}","gists_url":"https://api.github.com/users/mcetincompbio/gists{/gist_id}","starred_url":"https://api.github.com/users/mcetincompbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcetincompbio/subscriptions","organizations_url":"https://api.github.com/users/mcetincompbio/orgs","repos_url":"https://api.github.com/users/mcetincompbio/repos","events_url":"https://api.github.com/users/mcetincompbio/events{/privacy}","received_events_url":"https://api.github.com/users/mcetincompbio/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2018-09-19T08:58:44Z","updated_at":"2018-10-17T10:38:44Z","closed_at":null,"author_association":"NONE","body":"I am running the following command:\r\npython SNPbam2vcf.py ancAnatBam.list BonBarTep.vcf 1000G_D100KApart.list\r\n\r\nancAnatBam.list contains the paths of a list of Bam files.\r\n1000G_D100KApart.list is the snp list in the format requested.\r\n\r\nI get this error:\r\n\r\nTraceback (most recent call last):\r\n  File \"SNPbam2vcf.py\", line 247, in <module>\r\n    sample_name.append(samfiles[g].header['RG'][0]['SM'])\r\nKeyError: 'RG'\r\n\r\nPlease respond. "},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/comments/430578942","html_url":"https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15#issuecomment-430578942","issue_url":"https://api.github.com/repos/COMBINE-lab/maximum-likelihood-relatedness-estimation/issues/15","id":430578942,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMDU3ODk0Mg==","user":{"login":"kveeramah","id":13582227,"node_id":"MDQ6VXNlcjEzNTgyMjI3","avatar_url":"https://avatars1.githubusercontent.com/u/13582227?v=4","gravatar_id":"","url":"https://api.github.com/users/kveeramah","html_url":"https://github.com/kveeramah","followers_url":"https://api.github.com/users/kveeramah/followers","following_url":"https://api.github.com/users/kveeramah/following{/other_user}","gists_url":"https://api.github.com/users/kveeramah/gists{/gist_id}","starred_url":"https://api.github.com/users/kveeramah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kveeramah/subscriptions","organizations_url":"https://api.github.com/users/kveeramah/orgs","repos_url":"https://api.github.com/users/kveeramah/repos","events_url":"https://api.github.com/users/kveeramah/events{/privacy}","received_events_url":"https://api.github.com/users/kveeramah/received_events","type":"User","site_admin":false},"created_at":"2018-10-17T10:38:44Z","updated_at":"2018-10-17T10:38:44Z","author_association":"NONE","body":"Yes. You should preferably choose SNPs where the AF is >10% in CEU individuals.\n\n--\nKrishna R Veeramah, Ph.D.\nAssistant Professor\nDept of Ecology and Evolution\nStony Brook University\nRm 616, 650 Life Sciences Building\nStony Brook\nNY 11794-5245\nOffice: 631-632-1101\nCell: 510-207-1424\nE-mail: krishna.veeramah@stonybrook.edu\nhttp://life.bio.sunysb.edu/ee/veeramahlab\n\n> On Oct 17, 2018, at 3:57 AM, mcetincompbio <notifications@github.com> wrote:\n> \n> It seems like a great majority (possibly more than 95%) of the SNPS are 0/0 in all 5 individuals of the CEPH family.\n> \n> Maybe that's why.\n> \n> Should I try with a different set of snps?\n> \n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub, or mute the thread.\n"}}
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