{"action":"closed","issue":{"url":"https://api.github.com/repos/greenelab/pdx_exomeseq/issues/26","repository_url":"https://api.github.com/repos/greenelab/pdx_exomeseq","labels_url":"https://api.github.com/repos/greenelab/pdx_exomeseq/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/greenelab/pdx_exomeseq/issues/26/comments","events_url":"https://api.github.com/repos/greenelab/pdx_exomeseq/issues/26/events","html_url":"https://github.com/greenelab/pdx_exomeseq/issues/26","id":279968087,"number":26,"title":"Call Variants in \"Ambiguous\" assigned reads","user":{"login":"gwaygenomics","id":7340421,"avatar_url":"https://avatars3.githubusercontent.com/u/7340421?v=4","gravatar_id":"","url":"https://api.github.com/users/gwaygenomics","html_url":"https://github.com/gwaygenomics","followers_url":"https://api.github.com/users/gwaygenomics/followers","following_url":"https://api.github.com/users/gwaygenomics/following{/other_user}","gists_url":"https://api.github.com/users/gwaygenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/gwaygenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gwaygenomics/subscriptions","organizations_url":"https://api.github.com/users/gwaygenomics/orgs","repos_url":"https://api.github.com/users/gwaygenomics/repos","events_url":"https://api.github.com/users/gwaygenomics/events{/privacy}","received_events_url":"https://api.github.com/users/gwaygenomics/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-12-07T01:32:10Z","updated_at":"2018-02-18T23:17:33Z","closed_at":"2018-02-18T23:17:33Z","author_association":"MEMBER","body":"It is possible that mutations in highly conserved regions between human and mouse are not included in our final VCF file. Reads with these variants are likely to be assigned to \"ambiguous\" from `ngs_disambiguate`\r\n\r\nAs @huqiwen0313 noted in #24:\r\n\r\n> The reason I think these regions would be interesting is if variants appear in the conserved regions, they are more likely to be functionally related. I did not see a database list all of the cancer-associated variance in the conserved regions, but there are some related papers (e.g. https://www.nature.com/articles/srep22124, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919555/).\r\n\r\nIt will be good to run all downstream steps in the ambiguous sets as was performed with human.\r\n"}}
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