{"action":"created","issue":{"url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/134","repository_url":"https://api.github.com/repos/iqbal-lab-org/gramtools","labels_url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/134/labels{/name}","comments_url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/134/comments","events_url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/134/events","html_url":"https://github.com/iqbal-lab-org/gramtools/issues/134","id":331538622,"node_id":"MDU6SXNzdWUzMzE1Mzg2MjI=","number":134,"title":"Discover 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command finds new variation with respect to an inferred personal reference.\r\n\r\n#### Inputs\r\nThese are the inputs to this command:\r\n* a gram directory (generated from a VCF `vcf_build` and a reference `reference_build`)\r\n* an inferred personal reference `reference_infer` (output of the `infer` command; format: FASTA)\r\n* a set of reads.\r\n\r\n#### Procedure\r\nThe following is an outline of how this command works:\r\n1. `reference_infer` and reads are passed to cortex which generates a VCF. This VCF will be referred to as `vcf_cortex`.\r\n2. A new VCF file is generated by transposing `vcf_cortex` such that the reference is `reference_build` instead of `reference_infer`. This VCF file will be referred to as `vcf_discover`.\r\n\r\n#### Output\r\nDiscover produces a single VCF file as an output: `vcf_discover`. This VCF file uses `reference_build` as a reference.\r\n\r\n#### Notes\r\nEach entry within `vcf_cortex` can contain at most one alternative. Furthermore, these entries do not overlap. This should also hold true for `vcf_discover`."},"comment":{"url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/comments/396905844","html_url":"https://github.com/iqbal-lab-org/gramtools/issues/134#issuecomment-396905844","issue_url":"https://api.github.com/repos/iqbal-lab-org/gramtools/issues/134","id":396905844,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NjkwNTg0NA==","user":{"login":"rffrancon","id":5958289,"node_id":"MDQ6VXNlcjU5NTgyODk=","avatar_url":"https://avatars0.githubusercontent.com/u/5958289?v=4","gravatar_id":"","url":"https://api.github.com/users/rffrancon","html_url":"https://github.com/rffrancon","followers_url":"https://api.github.com/users/rffrancon/followers","following_url":"https://api.github.com/users/rffrancon/following{/other_user}","gists_url":"https://api.github.com/users/rffrancon/gists{/gist_id}","starred_url":"https://api.github.com/users/rffrancon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rffrancon/subscriptions","organizations_url":"https://api.github.com/users/rffrancon/orgs","repos_url":"https://api.github.com/users/rffrancon/repos","events_url":"https://api.github.com/users/rffrancon/events{/privacy}","received_events_url":"https://api.github.com/users/rffrancon/received_events","type":"User","site_admin":false},"created_at":"2018-06-13T11:32:18Z","updated_at":"2018-06-13T11:32:18Z","author_association":"MEMBER","body":"The `infer` command can generate either a VCF `vcf_infer` or FASTA `reference_infer` output. The `discover` command should take `vcf_infer` as an input and not `reference_infer`. This will make it easier to \"rebase\" the cortex output VCF `vcf_cortex` on to the reference found in the gram directory.\r\n\r\nWill update top comment."}}
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