User: ingrid.schulman

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Posts by ingrid.schulman

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Understanding Weight column in .cns files in cnvkit
... Hi, I'm having trouble interpretating the calls.cns files derived from running cnvkit. The weight is supposed to be a measure of how reliable the result is right? But what is considered being a small weight value and what would be a "good" one? Right now all my weight values are below zero but vari ...
cnvkit weight call written 10 months ago by ingrid.schulman0 • updated 10 months ago by Eric T.2.2k
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Problems using cnvkit for ctDNA targeted sequencing
... Hi, I have tried to use cnvkit to detect copynumbers in circulating tumor DNA samples. I used the "batch -m amplicon" command with both cancer and normal samples followed by "call" to get absolute copy numbers. The results doesn't correlate much with the "actual" copyumbers in my data (I also have w ...
cnvkit ctdna results written 10 months ago by ingrid.schulman0 • updated 10 months ago by Eric T.2.2k
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Comment: C: mergeSegments.pl varscan confusion !
... Has there been any progress on this? ...
written 11 months ago by ingrid.schulman0
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Using cnvkit for targeted amplicon sequencing
... Hi, I'm trying to use cnvkit python package to calculate copy numbers for targeted amplicon sequenced data. I have cancer samples and normal samples and would like to do a paired reference, is this possible to do with cnvkit and how do I do it? In the documentation I only find examples for TAS with ...
cnvkit targeted amplicon sequencing reference cnv written 12 months ago by ingrid.schulman0 • updated 11 months ago by Eric T.2.2k

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