{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/canvas/issues/13","repository_url":"https://api.github.com/repos/Illumina/canvas","labels_url":"https://api.github.com/repos/Illumina/canvas/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/canvas/issues/13/comments","events_url":"https://api.github.com/repos/Illumina/canvas/issues/13/events","html_url":"https://github.com/Illumina/canvas/issues/13","id":164163650,"number":13,"title":"Use the matched normal during \"Somatic-WGS\"?","user":{"login":"RichardCorbett","id":9285915,"avatar_url":"https://avatars.githubusercontent.com/u/9285915?v=3","gravatar_id":"","url":"https://api.github.com/users/RichardCorbett","html_url":"https://github.com/RichardCorbett","followers_url":"https://api.github.com/users/RichardCorbett/followers","following_url":"https://api.github.com/users/RichardCorbett/following{/other_user}","gists_url":"https://api.github.com/users/RichardCorbett/gists{/gist_id}","starred_url":"https://api.github.com/users/RichardCorbett/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RichardCorbett/subscriptions","organizations_url":"https://api.github.com/users/RichardCorbett/orgs","repos_url":"https://api.github.com/users/RichardCorbett/repos","events_url":"https://api.github.com/users/RichardCorbett/events{/privacy}","received_events_url":"https://api.github.com/users/RichardCorbett/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-07-06T20:14:59Z","updated_at":"2016-07-26T15:45:37Z","closed_at":null,"body":"Hey there,\r\nI don't see an option to include the aligned reads from the matched normal to help normalize the depths of the tumour read counts.    It does show up in your example of the \"Tumor-normal-enrichment\" command.    In my experience, having the matched normal helped normalize out some biases in read coverage that weren't properly modeled by GC, etc.   Is there a way to include the normal read depths when running \"somatic-WGS\" ?\r\n\r\nthanks,\r\nRIchard\r\n"},"comment":{"url":"https://api.github.com/repos/Illumina/canvas/issues/comments/235310599","html_url":"https://github.com/Illumina/canvas/issues/13#issuecomment-235310599","issue_url":"https://api.github.com/repos/Illumina/canvas/issues/13","id":235310599,"user":{"login":"sivakhno","id":1651457,"avatar_url":"https://avatars.githubusercontent.com/u/1651457?v=3","gravatar_id":"","url":"https://api.github.com/users/sivakhno","html_url":"https://github.com/sivakhno","followers_url":"https://api.github.com/users/sivakhno/followers","following_url":"https://api.github.com/users/sivakhno/following{/other_user}","gists_url":"https://api.github.com/users/sivakhno/gists{/gist_id}","starred_url":"https://api.github.com/users/sivakhno/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sivakhno/subscriptions","organizations_url":"https://api.github.com/users/sivakhno/orgs","repos_url":"https://api.github.com/users/sivakhno/repos","events_url":"https://api.github.com/users/sivakhno/events{/privacy}","received_events_url":"https://api.github.com/users/sivakhno/received_events","type":"User","site_admin":false},"created_at":"2016-07-26T15:45:37Z","updated_at":"2016-07-26T15:45:37Z","body":"We have considered using a matched normal sample for normalization / tumor – normal ratio calculations, but decided against it due to a number of factors below, there could still be a separate parameter in later releases to enable \"reference-based\" normalization\r\n\r\n1)     Non-reference CNV variants in normal samples can introduce spurious / false positive somatic calls\r\n2)     It would also increase Canvas runtime due to additional I/O and the coverage binning step for a normal sample \r\n3)     Will cause issues when tumour is FFPE and normal is fresh frozen"}}
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