{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2177","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2177/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2177/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2177/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2177","id":280428442,"number":2177,"title":"Tumour-only prioritization not working","user":{"login":"ameynert","id":6746627,"avatar_url":"https://avatars3.githubusercontent.com/u/6746627?v=4","gravatar_id":"","url":"https://api.github.com/users/ameynert","html_url":"https://github.com/ameynert","followers_url":"https://api.github.com/users/ameynert/followers","following_url":"https://api.github.com/users/ameynert/following{/other_user}","gists_url":"https://api.github.com/users/ameynert/gists{/gist_id}","starred_url":"https://api.github.com/users/ameynert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ameynert/subscriptions","organizations_url":"https://api.github.com/users/ameynert/orgs","repos_url":"https://api.github.com/users/ameynert/repos","events_url":"https://api.github.com/users/ameynert/events{/privacy}","received_events_url":"https://api.github.com/users/ameynert/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-12-08T09:37:13Z","updated_at":"2017-12-08T10:33:27Z","closed_at":null,"author_association":"NONE","body":"v1.0.6, YAML file template:\r\n\r\n```\r\ndetails:\r\n- algorithm:\r\n    aligner: bwa\r\n    background: /path/to/bcbio/genomes/Hsapiens/hg38/variation/1000G_omni2.5.vcf.gz\r\n    platform: illumina\r\n    quality_format: standard\r\n    umi_type: fastq_name\r\n    mark_duplicates: true\r\n    recalibrate: true\r\n    realign: false\r\n    remove_lcr: true\r\n    mixup_check: qsignature\r\n    kraken: minikraken\r\n    variantcaller: [vardict, mutect2, freebayes]\r\n    min_allele_fraction: 5\r\n    indelcaller: false\r\n    ensemble:\r\n      numpass: 2\r\n      use_filtered: false\r\n    effects: vep\r\n    effects_transcripts: canonical\r\n    tools_off: [gemini]\r\n    tools_on: [damage_filter]\r\n  analysis: variant2\r\n  genome_build: hg38\r\nupload:\r\n  dir: /path/to/upload\r\n```\r\n\r\nIdentical template YAML used under v1.0.5 and v1.0.6. In v.1.0.5, 16 panel sequenced samples resulted in 80 candidate somatic variants after tumour-only prioritization. The next set of 16 samples were processed under v1.0.6 and resulted in 2019 samples. Another 32 samples produced 6301 variants. Looking at the VCFs, the vast majority of variants are common - they have rsids and MAFs over 0.01 in the populations used by VEP."},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/350230451","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2177#issuecomment-350230451","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2177","id":350230451,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars1.githubusercontent.com/u/39391?v=4","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2017-12-08T10:33:27Z","updated_at":"2017-12-08T10:33:27Z","author_association":"OWNER","body":"Alison;\r\nThanks for the report and sorry about the issue. Prioritization needs to have the sample labelled as tumor to run, so this config would need to have:\r\n```\r\nmetadata:\r\n  phenotype: tumor\r\n```\r\nadded, and then it should correctly run it. You could add this and run your previous samples in place to get this added to them. Let us know if you run into any other issues."}}
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