cnvkit
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etal
Copy number variant detection from targeted DNA sequencing
Hi, I am looking for hg38 accessible bed file (access-5k-mappable.hg38.bed) in https://github.com/etal/cnvkit/tree/master/data and is missing. Can you please update it for downloading from [data/](https://github.com/etal/cnvkit/tree/master/data) or instruct me for generate this...
Hello, I need to compare different CNV callers before the segmentation step, and I would like for all of them to produce results on bins having the same size. Is...
Hello, I ran cnvkit on conda environment. Here's my command cnvkit.py batch $INPUT/$i".recal.bam" -n \ --targets $REF/bed/snuh_nicu_sort.bed \ --fasta $REF/hg19/hg19_1-22-X-Y-M.fa \ --access $CNVKIT/data/access-5k-mappable.hg19.bed \ --output-reference $FINAL/$i".cnn" \ --output-dir $FINAL Here's...
Hi, thank you for providing cnvkit and also funcitons to make the ouput compatible for gistic. It is really great to have that. I ran the seg command just fine...
I got the copy number of the target gene by the DPCR experience, and the result is 8. There are 4 normal and 2tumor samples. I try to use the...
Hi, all, my question is as follows, how can I solve it? thanks my command: cnvkit.py fix tumor.targetcoverage.cnn tumor.antitargetcoverage.cnn Reference.cnn -o tumor.cnr Processing target: samplename Traceback (most recent call last):...
cnary.py ``` def by_gene(self, ignore=params.IGNORE_GENE_NAMES): ignore += params.ANTITARGET_ALIASES start_idx = end_idx = None (only del in 0.9.9 ? Why?) ``` something wrong in genemetrics result ``` $ python3 cnvkit.py genemetrics...
Hello I tried to install cnvkit using conda. However, it is currently unfinished on the 3rd day. Only the process of "Examing conflicts ~~" is being repeated over and over...
the latest docker at https://hub.docker.com/r/etal/cnvkit/ is for version 0.9.8...can you upload one for 0.9.9?
I analysized one sample with 2p24.3 amplification and verified positive gene by FISH with cluster signal. WES had very high coverage (>60000, mean coverage 300). File tumor_sample.targetcoverage.cnn had high log2...
