cnvkit.readthedocs.io

CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.1 documentation

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

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CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.1 documentation | cnvkit.readthedocs.io Reviews

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Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

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1 cnvkit

2 stable

3 quick start

4 plots and graphics

5 additional scripts

6 tumor analysis

7 tumor heterogeneity

8 germline analysis

9 gender

10 bias corrections

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CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.1 documentation | cnvkit.readthedocs.io Reviews

https://cnvkit.readthedocs.io

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

INTERNAL PAGES

cnvkit.readthedocs.io

1

CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.0 documentation

http://cnvkit.readthedocs.io/en/v0.8.0

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

2

Bias corrections — CNVkit 0.8.5 documentation

http://cnvkit.readthedocs.io/en/stable/bias.html

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). The GC content and repeat-masked fraction of each bin are calculated during generation of the reference. From the user-supplied genome. The bias corrections are then performed in the reference. Genomic regions with extreme GC content, the fraction of sequence compos...

3

Whole-genome sequencing and targeted amplicon capture — CNVkit 0.8.5 documentation

http://cnvkit.readthedocs.io/en/stable/nonhybrid.html

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Targeted Amplicon Sequencing (TAS). Python API (cnvlib package). Whole-genome sequencing and targeted amplicon capture. Whole-genome sequencing and targeted amplicon capture. CNVkit is primarily designed for use on hybrid capture. WGS) and targeted amplicon sequencing. Instead of analyzing the ...

4

Calling copy number gains and losses — CNVkit 0.8.5 documentation

http://cnvkit.readthedocs.io/en/stable/calling.html

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). Calling copy number gains and losses. Calling copy number gains and losses. When using the gainloss. Command, choose a threshold to suit your needs depending on your knowledge of the sample’s purity, heterogeneity, and likely features of interest. As a sta...To eval...

5

Plots and graphics — CNVkit 0.8.5 documentation

http://cnvkit.readthedocs.io/en/stable/plots.html

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). Plot bin-level log2 coverages and segmentation calls together. Without any further arguments, this plots the genome-wide copy number in a form familiar to those who have used array CGH. Or their single-letter equivalents) focus the plot on the specified region:.

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github.com

GitHub - etal/cnvkit: Copy number variant detection from targeted DNA sequencing

https://github.com/etal/cnvkit

Copy number variant detection from targeted DNA sequencing. Http:/ cnvkit.readthedocs.org. Use Git or checkout with SVN using the web URL. Aug 24, 2016. Resurrect cnn updater.py script. Failed to load latest commit information. Cnary: privatize the method guess average depth. Aug 24, 2016. Data: GRCh37 mitochondrial chromosome is named "MT", not "M". Mar 21, 2016. Use conda travis env grid for CI (. May 16, 2016. Doc: start FAQ at end of quickstart page. Jul 19, 2016. Apr 27, 2016. Jul 17, 2014. Report s...

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CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.1 documentation

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

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