{"action":"created","issue":{"url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/68","repository_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict","labels_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/68/comments","events_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/68/events","html_url":"https://github.com/AstraZeneca-NGS/VarDict/issues/68","id":337500724,"node_id":"MDU6SXNzdWUzMzc1MDA3MjQ=","number":68,"title":"Very high false positive rate","user":{"login":"dancooke","id":1231781,"node_id":"MDQ6VXNlcjEyMzE3ODE=","avatar_url":"https://avatars2.githubusercontent.com/u/1231781?v=4","gravatar_id":"","url":"https://api.github.com/users/dancooke","html_url":"https://github.com/dancooke","followers_url":"https://api.github.com/users/dancooke/followers","following_url":"https://api.github.com/users/dancooke/following{/other_user}","gists_url":"https://api.github.com/users/dancooke/gists{/gist_id}","starred_url":"https://api.github.com/users/dancooke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dancooke/subscriptions","organizations_url":"https://api.github.com/users/dancooke/orgs","repos_url":"https://api.github.com/users/dancooke/repos","events_url":"https://api.github.com/users/dancooke/events{/privacy}","received_events_url":"https://api.github.com/users/dancooke/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-07-02T12:37:42Z","updated_at":"2018-07-12T15:05:53Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI'm currently evaluating VarDict on a synthetic tumour dataset similar to the ICGC DREAM set. I'm using VarDict version 1.5.2 with the following commands:\r\n\r\nCall variants:\r\n\r\n```shell\r\n$ VarDict \\\r\n    -G hs37d5.fa \\\r\n    -f 0.01 \\\r\n    -N NA12878.TUMOUR \\\r\n    -b \"NA12878.TUMOUR.60x.skin.bwa-mem.b37.bam|NA12878.NORMAL.30x.bwa.b37.bam\" \\\r\n    -z 0 -c 1 -S 2 -E 3 \\\r\n    hs37d5.chromosomes.bed \\\r\n    | testsomatic.R \\\r\n    | var2vcf_paired.pl \\\r\n      -N \"NA12878.TUMOUR|NA12878.NORMAL\" \\\r\n      -f 0.01 \\\r\n      | bgzip \\\r\n      > vardict.NA12878.syntumour.skin.b37.bwa.vcf.gz\r\n$ tabix vardict.NA12878.syntumour.skin.b37.bwa.vcf.gz\r\n```\r\n\r\nFilter somatics:\r\n\r\n```shell\r\n$ bcftools view \\\r\n    -i 'INFO/STATUS=\"StrongSomatic\"' \\\r\n    -f PASS \\\r\n    -Oz -o vardict.NA12878.syntumour.skin.b37.bwa.somatic.PASS.vcf.gz \\\r\n    vardict.NA12878.syntumour.skin.b37.bwa.vcf.gz\r\n$ tabix vardict.NA12878.syntumour.skin.b37.bwa.somatic.PASS.vcf.gz\r\n```\r\n\r\nAlthough VarDict achieves high sensitivity, the false positive rate is very high (FDR 0.25 compared with < 0.02 for all other callers tested). Am I doing something wrong?\r\n\r\nThanks,\r\nDan"},"comment":{"url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/comments/404544712","html_url":"https://github.com/AstraZeneca-NGS/VarDict/issues/68#issuecomment-404544712","issue_url":"https://api.github.com/repos/AstraZeneca-NGS/VarDict/issues/68","id":404544712,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDU0NDcxMg==","user":{"login":"chapmanb","id":39391,"node_id":"MDQ6VXNlcjM5Mzkx","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":"2018-07-12T15:05:53Z","updated_at":"2018-07-12T15:05:53Z","author_association":"MEMBER","body":"Dan -- thanks for this. Misclassifying germline as somatic is definitely a problem across callers, and is a limitation of not having the normal for effectively doing this. I'll definitely work on including octopus in the comparisons as an additional data point you can use for octopus versus VarDict in terms of specificity (at least for these harder cases). Thanks again."}}
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