Tool stats & trends
Looking to identify usage trends or leading experts?
|Interface||Command line interface|
|Restrictions to use||None|
|Input data||One or more DNA sequencing read alignments and the capture bait locations or a pre-built “reference” file.|
|Operating system||Unix/Linux, Mac OS, Windows|
|License||Apache License version 2.0|
DNAcopy, biopython, python, scipy, numpy, conda, pysam, matplotlib, bioconda, pandas, pyvcf, miniconda, anaconda, cnvkit, conda-forge
No version available
- person_outline Eric Talevich
Publications for CNVkit
Genomic features of renal cell carcinoma with venous tumor thrombus
[…] CNAs were inferred from whole exome sequencing data with cnvKit version 0.8.6 (git repository hash: 85774ac) with default parameter settings.Heterozygous SNPs were determined as those positions with alternative allele fraction between 0.3 and 0.7 in the res […]
Genomic characterization of chronic lymphocytic leukemia (CLL) in radiation exposed Chornobyl cleanup workers
[…] CNAs were analyzed using CNVkit  and off-target reads from the target area with capture probes. CNVkit was run with default parameters and female genome as reference. A threshold of 0.3 was applied to identify the signals f […]
Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal
[…] To estimate SCNAs, CNVkit v0.7.3 was performed with default parameter on paired tumour-normal sequencing data (). Outliers of the derived log2-ratio (logR) calls from CNVkit were detected and modified using Median Absol […]
Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal
[…] To estimate somatic copy number alterations, CNVkit v0.7.3 was performed with default parameter on paired tumour-normal sequencing data (). Outliers of the derived log2-ratio (logR) calls from CNVkit were detected and modified using Median Absol […]
Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers
[…] Copy number segmentations were generated by CNVkit using default settings (bcbio-nextgen v0.9.3). SCNA breakpoints were defined as the ends of non-diploid segments. Assuming tumor purity of 50%, the estimated mean purity of these tumors, non-di […]
Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS based analysis of hereditary cancer syndromes
[…] 35 samples tested positively using the MLPA analysis (). All CNVs including 18 samples with large BRCA1 deletions or duplications, 12 CNVs in CHEK2, four in PALB2 and one in TP53 were detected using CNVkit software in routine settings targeting 100X coverage (; ). This analysis also enabled to setup CNVkit thresholds indicating the presence of a deletion or a duplication. To estimate the number o […]
Looking to check out a full list of citations?
This software is very precise (specificity, sensitivity). I'm now using it in diagnostics, on small and large panels of genes.
the documentation is rich and well done. Recommended for immediate use!!