{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2171","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2171/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2171/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2171/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2171","id":278278696,"number":2171,"title":"Incorrect CNVkit output ","user":{"login":"choosehappy","id":9681868,"avatar_url":"https://avatars0.githubusercontent.com/u/9681868?v=4","gravatar_id":"","url":"https://api.github.com/users/choosehappy","html_url":"https://github.com/choosehappy","followers_url":"https://api.github.com/users/choosehappy/followers","following_url":"https://api.github.com/users/choosehappy/following{/other_user}","gists_url":"https://api.github.com/users/choosehappy/gists{/gist_id}","starred_url":"https://api.github.com/users/choosehappy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choosehappy/subscriptions","organizations_url":"https://api.github.com/users/choosehappy/orgs","repos_url":"https://api.github.com/users/choosehappy/repos","events_url":"https://api.github.com/users/choosehappy/events{/privacy}","received_events_url":"https://api.github.com/users/choosehappy/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":36,"created_at":"2017-11-30T21:38:27Z","updated_at":"2017-12-18T11:41:07Z","closed_at":"2017-12-06T13:06:48Z","author_association":"NONE","body":"I’ve used the cnvkit a few times, but this particular sample results in stating everything is at a loss.\r\n\r\nThis is the head T1.cns file produced by bcbio (i removed the gene column for clarity)\r\n\r\n```\r\nchromosome | start | end | gene | log2 | baf | depth | probes | weight\r\n-- | -- | -- | -- | -- | -- | -- | -- | --\r\nchr1 | 10044 | 3783855 | removed | -1.86927 | 0.402385 | 3.47617 | 3006 | 404.754\r\nchr1 | 3786057 | 12808529 | removed | -2.93556 | 0.446113 | 1.56538 | 8470 | 1231.48\r\nchr1 | 12810479 | 14874986 | removed | -4.6436 | 0.433824 | 0.933951 | 1538 | 225.929\r\nchr1 | 14876201 | 16524732 | removed | -2.55335 | 0.439711 | 1.89716 | 1584 | 229.988\r\nchr1 | 16525961 | 16962159 | removed | -0.14769 | 0.263566 | 4.08855 | 297 | 42.2095\r\nchr1 | 16962525 | 46822896 | removed | -3.13869 | 0.444444 | 1.5238 | 26862 | 3916.87\r\nchr1 | 46824333 | 51700063 | removed | -4.49549 | 0.449153 | 0.982765 | 3712 | 547.092\r\n```\r\n\r\nnote that all of the log2 values are quite negative (-call.cns is similar)\r\n\r\nand this is the result of running cnvkit manually:\r\n\r\n```\r\nchromosome | start | end | gene | log2 | depth | probes | weight\r\n-- | -- | -- | -- | -- | -- | -- | --\r\nchr1 | 65409 | 7106529 | X | -0.06439 | 105.197 | 1521 | 522.478\r\nchr1 | 7107029 | 1.22E+08 | X |   |   |   |  \r\nchr1 | 1.22E+08 | 1.25E+08 | X | 1.19374 | 3.32145 | 16 | 7.01406\r\nchr1 | 1.44E+08 | 1.52E+08 | X |   |   |   |  \r\nchr1 | 1.52E+08 | 1.52E+08 | X | 0.595503 | 239.102 | 74 | 21.886\r\nchr1 | 1.52E+08 | 2.48E+08 | X |   |   |   |  \r\nchr1 | 2.48E+08 | 2.49E+08 | X | 0.304078 | 156.569 | 184 | 63.7607\r\nchr2 | 41359 | 93085490 | X |   |   |   |  \r\nchr2 | 94573375 | 1.79E+08 | X |   |   |   |  \r\nchr2 | 1.79E+08 | 1.79E+08 | X | 0.168907 | 216.203 | 540 | 173.011\r\nchr2 | 1.79E+08 | 2E+08 | X | 0.031598 | 92.5111 | 1717 | 642.207\r\n```\r\n\r\nwhile some of the columns are 0, the results are much more close to accurate \r\n\r\nthis is the manual command, which i don't think is particularly unique and uses the bcbio generated bam files\r\n\r\n`cnvkit.py batch final/T1/T1-ready.bam --normal final/N1/N1-ready.bam  -p 8 --targets ../S04380110_Padded_hg38_trimmed.bed  --fasta /mnt/biodata/genomes/Hsapiens/hg38/seq/hg38.fa --output-dir ./cnvkit/ --diagram –scatter`\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/352402746","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2171#issuecomment-352402746","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2171","id":352402746,"user":{"login":"choosehappy","id":9681868,"avatar_url":"https://avatars0.githubusercontent.com/u/9681868?v=4","gravatar_id":"","url":"https://api.github.com/users/choosehappy","html_url":"https://github.com/choosehappy","followers_url":"https://api.github.com/users/choosehappy/followers","following_url":"https://api.github.com/users/choosehappy/following{/other_user}","gists_url":"https://api.github.com/users/choosehappy/gists{/gist_id}","starred_url":"https://api.github.com/users/choosehappy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choosehappy/subscriptions","organizations_url":"https://api.github.com/users/choosehappy/orgs","repos_url":"https://api.github.com/users/choosehappy/repos","events_url":"https://api.github.com/users/choosehappy/events{/privacy}","received_events_url":"https://api.github.com/users/choosehappy/received_events","type":"User","site_admin":false},"created_at":"2017-12-18T11:41:07Z","updated_at":"2017-12-18T11:41:07Z","author_association":"NONE","body":"Similar results, at least this time the commands use the bed file:\r\n\r\n```\r\nroot@51853b033dc8:/data/CNV.valid/P1/work# grep target.bed log/bcbio-nextgen-commands.log | grep cnvkit.py\r\n[2017-12-17T22:52Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmp7B2rGF && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py target /data/CNV.valid/P1/work/bedprep/N1-variant_regions.quantized-vrsubset-callableblocks.bed --split -o /data/CNV.valid/P1/work/bcbiotx/tmp7B2rGF/N1-target.bed --avg-size 250\r\n[2017-12-17T22:53Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpHaAz9W && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py antitarget -g /data/CNV.valid/P1/work/regions/b1-analysis_blocks.bed /data/CNV.valid/P1/work/bedprep/N1-variant_regions.quantized-vrsubset-callableblocks.bed -o /data/CNV.valid/P1/work/bcbiotx/tmpHaAz9W/N1-antitarget.bed --avg-size 1000000\r\n[2017-12-17T22:53Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmp7v3UWi && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py target /data/CNV.valid/P1/work/bedprep/N1-variant_regions.quantized-vrsubset-callableblocks.bed --split -o /data/CNV.valid/P1/work/bcbiotx/tmp7v3UWi/T1-target.bed --avg-size 250\r\n[2017-12-17T22:54Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpwLTweU && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py antitarget -g /data/CNV.valid/P1/work/regions/b1-analysis_blocks.bed /data/CNV.valid/P1/work/bedprep/N1-variant_regions.quantized-vrsubset-callableblocks.bed -o /data/CNV.valid/P1/work/bcbiotx/tmpwLTweU/T1-antitarget.bed --avg-size 1000000\r\n[2017-12-18T10:56Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpuD17Il && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py target /data/CNV.valid/P1/work/bedprep/S04380110_Padded_hg38_trimmed.bed --split -o /data/CNV.valid/P1/work/bcbiotx/tmpuD17Il/N1-target.bed --avg-size 250\r\n[2017-12-18T10:56Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpvDbS9E && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py antitarget -g /data/CNV.valid/P1/work/regions/b1-analysis_blocks.bed /data/CNV.valid/P1/work/bedprep/S04380110_Padded_hg38_trimmed.bed -o /data/CNV.valid/P1/work/bcbiotx/tmpvDbS9E/N1-antitarget.bed --avg-size 350000\r\n[2017-12-18T10:56Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpBAcqBP && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py target /data/CNV.valid/P1/work/bedprep/S04380110_Padded_hg38_trimmed.bed --split -o /data/CNV.valid/P1/work/bcbiotx/tmpBAcqBP/T1-target.bed --avg-size 250\r\n[2017-12-18T10:56Z] export TMPDIR=/data/CNV.valid/P1/work/bcbiotx/tmpvfJwYc && /usr/local/share/bcbio-nextgen/anaconda/bin/cnvkit.py antitarget -g /data/CNV.valid/P1/work/regions/b1-analysis_blocks.bed /data/CNV.valid/P1/work/bedprep/S04380110_Padded_hg38_trimmed.bed -o /data/CNV.valid/P1/work/bcbiotx/tmpvfJwYc/T1-antitarget.bed --avg-size 350000\r\n\r\n```\r\n\r\nin the dropbox, i replaced the structural directory with this new version:\r\n\r\nhttps://www.dropbox.com/sh/8opt8h7heuw9k51/AABIcavnIv5bbyVSagKEc_hea?dl=0\r\n\r\n"}}
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