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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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question about the segment threshold #852

Open litun-fkby opened 11 months ago

litun-fkby commented 11 months ago

Hi, i used the cnvkit.py segment to generate the cns file form cnr，and to call the cnv number . So i have some question about the segment. The cnvkit version is 0.9.9 The segment command is : cnvkit segment sample.fix.cnr -p 20s --drop-low-coverage -m hmm-tumor -o sample.segment.hmm_tumor.cns cnvkit call sample.segment.hmm_tumor.cns -t=-1.1,-0.5,0.4,0.9 -o sample.call.hmm_tumor.cns cnvkit scatter sample.fix.cnr -s sample.segment.hmm_tumor.cns -g ERBB2 -o sample.cnv.scatter.ERBB2.png The png as follow: image

And the log2-ratio in cns seem to be lower than the log2-ratio in cnr , and i notices that "cnvkit.py segment " have the option -t to set the threshold , so my question is: 1.The default value for the -t . 2.The ERBB2 log2-ratio in cns may be affected by the upstream and downstream gene log2-ratio, how can i set the threshold to make the segment in each gene。 And here is the cnr file and cns file : sample.call.hmm_tumor.cns.txt sample.fix.cnr.txt

Hope your reply. Thanks!

gevro commented 1 month ago

Hello, I am also curious if anyone knows the default value for the segment command's threshold parameter?