Debian 12 (Bookworm) native package

cnvkit

Copy number variant detection from targeted DNA sequencing

Packages / Debian 12 (Bookworm) / science / cnvkit

[Source: cnvkit]

Package: cnvkit (0.9.9-2+b1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [cnvkit.readthedocs.org]

Copy number variant detection from targeted DNA sequencing

Other Packages Related to cnvkit:

dep: [python3-biopython]
Python3 library for bioinformatics
dep: [python3-joblib]
tools to provide lightweight pipelining in Python
dep: [python3-matplotlib]
Python based plotting system in a style similar to Matlab (Python 3)
dep: [python3-networkx]
tool to create, manipulate and study complex networks (Python3)
dep: [python3-numpy]
Fast array facility to the Python 3 language
dep: [python3-pandas]
data structures for "relational" or "labeled" data
dep: [python3-pomegranate]
Fast, flexible and easy to use probabilistic modelling
dep: [python3-pyfaidx]
efficient random access to fasta subsequences for Python 3
dep: [python3-pysam]
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
dep: [python3-reportlab]
ReportLab library to create PDF documents using Python3
dep: [python3-scipy]
scientific tools for Python 3
dep: [python3-sklearn]
Python modules for machine learning and data mining - Python 3
dep: [python3] [any]
interactive high-level object-oriented language (default python3 version)
dep: [r-bioc-dnacopy]
R package: DNA copy number data analysis

Download cnvkit

Architecture	Package Size	Installed Size	Files
amd64	15 MiB	67 MiB	[list of files]

Percorsi file del pacchetto (192)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/bin/cnvkit
/usr/bin/cnvkit-cnv_annotate
/usr/bin/cnvkit-cnv_expression_correlate
/usr/bin/cnvkit-cnv_updater
/usr/bin/cnvkit-genome_instability_index
/usr/bin/cnvkit-guess_baits
/usr/bin/cnvkit-reference2targets
/usr/bin/cnvkit-skg_convert
/usr/bin/snpfilter.sh
/usr/lib/debian-med/bin/cnvkit.py
/usr/lib/python3/dist-packages/CNVkit-0.9.9.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/CNVkit-0.9.9.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/CNVkit-0.9.9.egg-info/requires.txt
/usr/lib/python3/dist-packages/CNVkit-0.9.9.egg-info/top_level.txt
/usr/lib/python3/dist-packages/cnvlib/access.py
/usr/lib/python3/dist-packages/cnvlib/antitarget.py
/usr/lib/python3/dist-packages/cnvlib/autobin.py
/usr/lib/python3/dist-packages/cnvlib/batch.py
/usr/lib/python3/dist-packages/cnvlib/bintest.py
/usr/lib/python3/dist-packages/cnvlib/call.py
/usr/lib/python3/dist-packages/cnvlib/cluster.py
/usr/lib/python3/dist-packages/cnvlib/cmdutil.py
/usr/lib/python3/dist-packages/cnvlib/cnary.py
/usr/lib/python3/dist-packages/cnvlib/commands.py
/usr/lib/python3/dist-packages/cnvlib/core.py
/usr/lib/python3/dist-packages/cnvlib/coverage.py
/usr/lib/python3/dist-packages/cnvlib/descriptives.py
/usr/lib/python3/dist-packages/cnvlib/diagram.py
/usr/lib/python3/dist-packages/cnvlib/export.py
/usr/lib/python3/dist-packages/cnvlib/fix.py
/usr/lib/python3/dist-packages/cnvlib/heatmap.py
/usr/lib/python3/dist-packages/cnvlib/importers.py
/usr/lib/python3/dist-packages/cnvlib/import_rna.py
/usr/lib/python3/dist-packages/cnvlib/__init__.py
/usr/lib/python3/dist-packages/cnvlib/metrics.py
/usr/lib/python3/dist-packages/cnvlib/parallel.py
/usr/lib/python3/dist-packages/cnvlib/params.py
/usr/lib/python3/dist-packages/cnvlib/plots.py
/usr/lib/python3/dist-packages/cnvlib/reference.py
/usr/lib/python3/dist-packages/cnvlib/reports.py
/usr/lib/python3/dist-packages/cnvlib/rna.py
/usr/lib/python3/dist-packages/cnvlib/samutil.py
/usr/lib/python3/dist-packages/cnvlib/scatter.py
/usr/lib/python3/dist-packages/cnvlib/segfilters.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/cbs.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/flasso.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/haar.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/hmm.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/__init__.py
/usr/lib/python3/dist-packages/cnvlib/segmentation/none.py
/usr/lib/python3/dist-packages/cnvlib/segmetrics.py
/usr/lib/python3/dist-packages/cnvlib/smoothing.py
/usr/lib/python3/dist-packages/cnvlib/target.py
/usr/lib/python3/dist-packages/cnvlib/vary.py
/usr/lib/python3/dist-packages/cnvlib/_version.py
/usr/lib/python3/dist-packages/skgenome/chromsort.py
/usr/lib/python3/dist-packages/skgenome/combiners.py
/usr/lib/python3/dist-packages/skgenome/gary.py
/usr/lib/python3/dist-packages/skgenome/__init__.py
/usr/lib/python3/dist-packages/skgenome/intersect.py
/usr/lib/python3/dist-packages/skgenome/merge.py
/usr/lib/python3/dist-packages/skgenome/rangelabel.py
/usr/lib/python3/dist-packages/skgenome/subdivide.py
/usr/lib/python3/dist-packages/skgenome/subtract.py
/usr/lib/python3/dist-packages/skgenome/tabio/bedio.py
/usr/lib/python3/dist-packages/skgenome/tabio/genepred.py
/usr/lib/python3/dist-packages/skgenome/tabio/gff.py
/usr/lib/python3/dist-packages/skgenome/tabio/__init__.py
/usr/lib/python3/dist-packages/skgenome/tabio/picard.py
/usr/lib/python3/dist-packages/skgenome/tabio/seg.py
/usr/lib/python3/dist-packages/skgenome/tabio/seqdict.py
/usr/lib/python3/dist-packages/skgenome/tabio/tab.py
/usr/lib/python3/dist-packages/skgenome/tabio/textcoord.py
/usr/lib/python3/dist-packages/skgenome/tabio/util.py
/usr/lib/python3/dist-packages/skgenome/tabio/vcfio.py
/usr/lib/python3/dist-packages/skgenome/tabio/vcfsimple.py
/usr/share/doc/cnvkit/changelog.Debian.amd64.gz
/usr/share/doc/cnvkit/changelog.Debian.arm64.gz
/usr/share/doc/cnvkit/changelog.Debian.gz
/usr/share/doc/cnvkit/copyright
/usr/share/doc/cnvkit/examples/data/access-10kb.hg19.bed
/usr/share/doc/cnvkit/examples/data/access-5k-mappable.grch37.bed
/usr/share/doc/cnvkit/examples/data/access-5k-mappable.hg19.bed
/usr/share/doc/cnvkit/examples/data/ensembl-gene-info.hg38.tsv
/usr/share/doc/cnvkit/examples/data/interval-exome.antitarget-9-90kb.bed
/usr/share/doc/cnvkit/examples/data/interval-exome.target-267.bed
/usr/share/doc/cnvkit/examples/data/interval-nv2.antitarget-15-150kb.bed
/usr/share/doc/cnvkit/examples/data/interval-nv2.target-267.bed
/usr/share/doc/cnvkit/examples/data/tcga-skcm.cnv-expr-corr.tsv
/usr/share/doc/cnvkit/examples/test/bintest.makefile
/usr/share/doc/cnvkit/examples/test/clustering.makefile
/usr/share/doc/cnvkit/examples/test/.coveragerc
/usr/share/doc/cnvkit/examples/test/formats/acgh-log10.seg
/usr/share/doc/cnvkit/examples/test/formats/amplicon.bed
/usr/share/doc/cnvkit/examples/test/formats/amplicon.cnr
/usr/share/doc/cnvkit/examples/test/formats/amplicon.cns
/usr/share/doc/cnvkit/examples/test/formats/amplicon.text
/usr/share/doc/cnvkit/examples/test/formats/baits-funky.bed
/usr/share/doc/cnvkit/examples/test/formats/blank.vcf
/usr/share/doc/cnvkit/examples/test/formats/chrM-Y-trunc.hg19.fa
/usr/share/doc/cnvkit/examples/test/formats/cl_seq.cns
/usr/share/doc/cnvkit/examples/test/formats/cw-tr-log2.seg
/usr/share/doc/cnvkit/examples/test/formats/dac-my.bed
/usr/share/doc/cnvkit/examples/test/formats/empty
/usr/share/doc/cnvkit/examples/test/formats/example.gff
/usr/share/doc/cnvkit/examples/test/formats/f-on-f.cns
/usr/share/doc/cnvkit/examples/test/formats/f-on-m.cns
/usr/share/doc/cnvkit/examples/test/formats/gatk-emptyalt.vcf
/usr/share/doc/cnvkit/examples/test/formats/GRCh37_BRAF.gff.gz
/usr/share/doc/cnvkit/examples/test/formats/m-on-f.cns
/usr/share/doc/cnvkit/examples/test/formats/m-on-m.cns
/usr/share/doc/cnvkit/examples/test/formats/my-refflat.bed
/usr/share/doc/cnvkit/examples/test/formats/my-targets.bed
/usr/share/doc/cnvkit/examples/test/formats/na12878-chrM-Y-trunc.bam
/usr/share/doc/cnvkit/examples/test/formats/na12878_na12882_mix.vcf
/usr/share/doc/cnvkit/examples/test/formats/nosample.vcf
/usr/share/doc/cnvkit/examples/test/formats/nv2_baits.interval_list
/usr/share/doc/cnvkit/examples/test/formats/nv3.cns
/usr/share/doc/cnvkit/examples/test/formats/nv3.n3.results
/usr/share/doc/cnvkit/examples/test/formats/p2-20_1.cnr
/usr/share/doc/cnvkit/examples/test/formats/p2-20_2.cnr
/usr/share/doc/cnvkit/examples/test/formats/reference-tr.cnn
/usr/share/doc/cnvkit/examples/test/formats/refflat-mini.txt
/usr/share/doc/cnvkit/examples/test/formats/tr95t.cns
/usr/share/doc/cnvkit/examples/test/formats/tr95t.segmetrics.cns
/usr/share/doc/cnvkit/examples/test/formats/warning.seg
/usr/share/doc/cnvkit/examples/test/formats/wgs-chr17.cnr
/usr/share/doc/cnvkit/examples/test/Makefile
/usr/share/doc/cnvkit/examples/test/picard/p1-21_1.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_1.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_2.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_2.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_3.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_3.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_4.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_4.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_5.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p1-21_5.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_1.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_1.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_2.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_2.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_3.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_3.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_4.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_4.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_5.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-20_5.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_1.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_1.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_2.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_2.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_5.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-5_5.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_1.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_1.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_2.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_2.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_5.antitargetcoverage.csv
/usr/share/doc/cnvkit/examples/test/picard/p2-9_5.targetcoverage.csv
/usr/share/doc/cnvkit/examples/test/regions.bed
/usr/share/doc/cnvkit/examples/test/test_cnvlib.py
/usr/share/doc/cnvkit/examples/test/test_commands.py
/usr/share/doc/cnvkit/examples/test/test_genome.py
/usr/share/doc/cnvkit/examples/test/test_io.py
/usr/share/doc/cnvkit/examples/test/test_r.py
/usr/share/man/man1/cnvkit.1.gz
/usr/share/man/man1/cnvkit-access.1.gz
/usr/share/man/man1/cnvkit-antitarget.1.gz
/usr/share/man/man1/cnvkit-autobin.1.gz
/usr/share/man/man1/cnvkit-batch.1.gz
/usr/share/man/man1/cnvkit-bintest.1.gz
/usr/share/man/man1/cnvkit-breaks.1.gz
/usr/share/man/man1/cnvkit-call.1.gz
/usr/share/man/man1/cnvkit-coverage.1.gz
/usr/share/man/man1/cnvkit-diagram.1.gz
/usr/share/man/man1/cnvkit-export.1.gz
/usr/share/man/man1/cnvkit-fix.1.gz
/usr/share/man/man1/cnvkit-genemetrics.1.gz
/usr/share/man/man1/cnvkit-heatmap.1.gz
/usr/share/man/man1/cnvkit-import-picard.1.gz
/usr/share/man/man1/cnvkit-import-rna.1.gz
/usr/share/man/man1/cnvkit-import-seg.1.gz
/usr/share/man/man1/cnvkit-import-theta.1.gz
/usr/share/man/man1/cnvkit-metrics.1.gz
/usr/share/man/man1/cnvkit-reference.1.gz
/usr/share/man/man1/cnvkit-reference2targets.1.gz
/usr/share/man/man1/cnvkit-scatter.1.gz
/usr/share/man/man1/cnvkit-segment.1.gz
/usr/share/man/man1/cnvkit-segmetrics.1.gz
/usr/share/man/man1/cnvkit-sex.1.gz
/usr/share/man/man1/cnvkit-target.1.gz

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Usa questo pacchetto

OpenFactory può avviare questo sistema operativo in una macchina virtuale del browser, o iniziare una costruzione che include il nome nativo del pacchetto di questo record.

Prova Debian 12 (Bookworm) nel browser Crea un'immagine che include cnvkit

Versioni, suite e repository

Ogni riga è metadato dell'indice pacchetti per una versione, architettura, suite e repository. Nomi, URL e dimensioni arrivano dalla fonte; un link è un punto di recupero mutabile, non una redistribuzione OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
0.9.9-2+b1	bookworm / main	amd64	Debian 12 · main · amd64	15 MiB	67 MiB	pool/main/c/cnvkit/cnvkit_0.9.9-2+b1_amd64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Checksum e date di osservazione

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

0.9.9-2+b1 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'b773bb7977d6fc9462b53b684aa74b7bd980387e48df07461a504d12742fcda0' 'cnvkit_0.9.9-2+b1_amd64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Completezza del record

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Fonti e provenienza

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified