{"action":"created","issue":{"url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/8","repository_url":"https://api.github.com/repos/Griffan/VerifyBamID","labels_url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/8/comments","events_url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/8/events","html_url":"https://github.com/Griffan/VerifyBamID/issues/8","id":316218972,"number":8,"title":"Using `--PileupFile` results in wildly incorrect contamination estimate","user":{"login":"jrandall","id":458361,"avatar_url":"https://avatars3.githubusercontent.com/u/458361?v=4","gravatar_id":"","url":"https://api.github.com/users/jrandall","html_url":"https://github.com/jrandall","followers_url":"https://api.github.com/users/jrandall/followers","following_url":"https://api.github.com/users/jrandall/following{/other_user}","gists_url":"https://api.github.com/users/jrandall/gists{/gist_id}","starred_url":"https://api.github.com/users/jrandall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrandall/subscriptions","organizations_url":"https://api.github.com/users/jrandall/orgs","repos_url":"https://api.github.com/users/jrandall/repos","events_url":"https://api.github.com/users/jrandall/events{/privacy}","received_events_url":"https://api.github.com/users/jrandall/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-04-20T10:44:59Z","updated_at":"2018-04-22T21:57:28Z","closed_at":"2018-04-22T19:20:46Z","author_association":"NONE","body":"This is what happens if you generate an `--OutputPileup` using VerifyBamID and then process that output using `--PileupFile` (on a rather contaminated sample):\r\n```\r\n$ VerifyBamID --BamFile 17995_6#10.bam --UDPath /resource/hgdp.10k.b38.vcf.gz.dat.UD --BedPath /resource/hgdp.10k.b38.vcf.gz.dat.bed --MeanPath /resource/hgdp.10k.b38.vcf.gz.dat.mu --Reference /data/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa --Output 17995_6#10.vbid2.hgdp.10k.out --OutputPileup\r\n$ cat 17995_6#10.vbid2.hgdp.10k.out.selfSM\r\n#SEQ_ID RG      CHIP_ID #SNPS   #READS  AVG_DP  FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF   RDPHET   RDPALT\r\nEGAN00001217480 NA      NA      9997    29278   2.92868 0.0802537       -13398.2        -13499.5        NA      NA      NA      NA      NA       NA      NA      NA      NA      NA\r\n$ VerifyBamID --PileupFile 17995_6#10.vbid2.hgdp.10k.out.Pileup --UDPath /resource/hgdp.10k.b38.vcf.gz.dat.UD --BedPath /resource/hgdp.10k.b38.vcf.gz.dat.bed --MeanPath /resource/hgdp.10k.b38.vcf.gz.dat.mu --Reference /data/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa --Output 17995_6#10.vbid2.hgdp.10k.from-vbid2-pileup.out\r\n$ cat 17995_6#10.vbid2.hgdp.10k.pileup.out.selfSM\r\n#SEQ_ID RG      CHIP_ID #SNPS   #READS  AVG_DP  FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF   RDPHET   RDPALT\r\n        NA      NA      9997    1803135200      4.59121e-41     2.60408e-07     -180050 -196712 NA      NA      NA      NA      NA      NA       NA      NA      NA      NA\r\n```\r\n\r\nI've shown this example for the sake of reproducibility, but I find the same problem when generating a pileup with samtools. Is contamination estimation broken when using `--PileupFile`? "},"comment":{"url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/comments/383415546","html_url":"https://github.com/Griffan/VerifyBamID/issues/8#issuecomment-383415546","issue_url":"https://api.github.com/repos/Griffan/VerifyBamID/issues/8","id":383415546,"user":{"login":"jrandall","id":458361,"avatar_url":"https://avatars3.githubusercontent.com/u/458361?v=4","gravatar_id":"","url":"https://api.github.com/users/jrandall","html_url":"https://github.com/jrandall","followers_url":"https://api.github.com/users/jrandall/followers","following_url":"https://api.github.com/users/jrandall/following{/other_user}","gists_url":"https://api.github.com/users/jrandall/gists{/gist_id}","starred_url":"https://api.github.com/users/jrandall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrandall/subscriptions","organizations_url":"https://api.github.com/users/jrandall/orgs","repos_url":"https://api.github.com/users/jrandall/repos","events_url":"https://api.github.com/users/jrandall/events{/privacy}","received_events_url":"https://api.github.com/users/jrandall/received_events","type":"User","site_admin":false},"created_at":"2018-04-22T21:57:28Z","updated_at":"2018-04-22T21:57:28Z","author_association":"NONE","body":"The commit currently tagged 1.0.3 is from before the fix: https://github.com/Griffan/VerifyBamID/tree/1.0.3 \r\n\r\nPerhaps you could delete the 1.0.3 tag and re-tag it as 6c7894cb ?"}}
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