Comments (3)
MicrobioSee
commented on August 13, 2024
Do you get the answers? I also face your question.
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28rietd
commented on August 13, 2024
Unfortunately the parameters used for the filtering are currently hard-coded in this file (L3-L5):
Line 1 in 0f827c0
I would also be in favour of being able to change the default parameter settings.
In addition, would it also be possible to write the masked_bins to an output file instead of stdout, as now no output is returned if the list exceeds 500 bins?
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WortJohn
commented on August 13, 2024
Thank you very much. It is a good idea for saving the filtered bins because the cluster signal maybe have very high log2ratio in itself. It may be a true amplification or deletion signal. If user can change the default parameter settings, cnvkit will be more perfect.
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Related Issues (20)
- Calculating non-integer copy number variations
- A question about purity assumption in the Docs
- Docker image of cnvkit does not contain additional scripts HOT 3
- We could not set the gender of the sample correctly in reference.py HOT 2
- Why adding a pseudocount of flat reference to the aggregated reference?
- sex inference and X chromosome copy number
- CNVkit for RNA-seq: log2 in *.cnr file is all zero
- Error Installing CNVKit via Miniconda HOT 1
- Can I use cnvkit software to evaluate the copy number of genes ？
- TypeError and AttributeError when running 'cnvkit.py target baits.bed --annotate refFlat.txt --split -o targets.bed'
- question about the segment threshold
- cnvkit for multiple wgs cohort
- cnvkit.py export bed
- What's the mean of CN column？
- What format is the input bam file?
- what are the steps for Germline and Somatic CNV detection using CNVkit?
- Adding gene diagram to heat map
- Smoothing window fraction fix results in noisier data in targeted sequencing panel? HOT 1
- TypeError: batch_run_sample() takes from 16 to 17 positional arguments but 18 were given HOT 1
- sex allocation incorrect for males; antitarget used over target
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