User: alice.choury

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alice.choury50
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Posts by alice.choury

<prev • 14 results • page 1 of 2 • next >
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Comment: C: CNVkit : small CNV calling
... In my experiences, we can detect cnv for single exon for constitutional samples. We use capture, amplicon doesn't works well. The target is cut bin of 20 bases. The antitarget is cut depending of the depth and the on-target. (We have 100X and 70% on-target so we cut around 20000 bases) And then ...
written 9 months ago by alice.choury50
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Explications about call function of CNVkit
... I try to explain in the most just way possible the different modes of the call function. Please tell me if I am wrong and complete the information if necessary. The call function allows the estimation of the absolute number of copies for each segment. There are two modes of calculation: - the thr ...
cnvkit call written 13 months ago by alice.choury50 • updated 13 months ago by Eric T.2.1k
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Comment: C: How is the "weight" calculated by CNVkit ?
... All of my apologies, thank you for your answer. ...
written 13 months ago by alice.choury50
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How is the "weight" calculated by CNVkit ?
... Hello, We search a kind of score whilch can eliminates many FP call in CNVkit results. We think that the weight can be used. We search a signification of this weight, an equation. In the manual of CNVkit, we found this extract : A weight is assigned to each remaining bin depending on: 1. The s ...
cnvkit weight cnv written 13 months ago by alice.choury50 • updated 13 months ago by Eric T.2.1k
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Comment: C: No call for exomes analysis
... It appears that the -t 0.05 option will show CNVs. I will continue with my analysis and keep you informed of the results. Thank you ...
written 14 months ago by alice.choury50
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Comment: C: No call for exomes analysis
... I would like to believe that all the calls are not all true positive but from there to believe that they are all false positives .... ...
written 14 months ago by alice.choury50
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No call for exomes analysis
... Hello, I'm trying to run CNVkit with 20 exomes of patient with Alzheimer disease. This exomes were screening by cytoscan and have many CNV. I have no négative pool so I make a baseline with this 20 exomes. I use the algorithm Flasso because CBS is not installed in my computer. After I use the r ...
exome cnvkit written 14 months ago by alice.choury50 • updated 14 months ago by Eric T.2.1k
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Draw centromere on chromosome scatter plot
... Hello, I run CNVkit with my somatic data. I draw scatter plot, of the chromosomes. Sometimes the segment is very long and I think there is maybe du to a CNV in a arm of a chromosome. So I want to separate the different arms of a chromosome in my plot. My idea is to show the centromere of the chromo ...
cnvkit plot cnv somatic written 15 months ago by alice.choury50 • updated 15 months ago by Eric T.2.1k
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Answer: A: Format of VCF for CNVkit call fonction and results
... Hello , I looked for a way to get a VCF (from lofreq) to the proper input format for CNVkit but to no avail. I have seen in the code that the frequency of the alleles are calculated from the VCF data. Now in my VCF I already have the AF calculated. Would not it be simpler to recover this value dir ...
written 16 months ago by alice.choury50
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Comment: C: CNVkit : small CNV calling
... Our capture is about 420 kb (only 35 gènes) . We sequence samples with a depth of coverage about 300b. Finally the 2 CNV detected (no false positives) have a size of 2411 and 98 bases. Two other CNVs of 1 exon were tested, and they could not be detected. They measure 54 and 53bp. For the command ...
written 16 months ago by alice.choury50

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