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clincnv2vcf

CNV2VCF is a tool to convert output of ClinCNV to VCF format.

https://github.com/mhh-humangenetik/clincnv2vcf

Science Score: 67.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

CNV2VCF is a tool to convert output of ClinCNV to VCF format.

Basic Info
  • Host: GitHub
  • Owner: MHH-Humangenetik
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 172 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 3 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

CNV2VCF

GitHub release (latest by date including pre-releases) DOI License: MIT Code style: black

CNV2VCF is a tool to convert output of ClinCNV to VCF format.

DEL/DUP interpretation is not (yet) gender aware for the X chromosome.

Custom info fields

The following custom INFO fields are added to the VCF: - NOREGIONS: Number of regions in the CNV (noofregions) - PAF: Potential allelic fraction (potentialAF) - GENES: List of genes affected by the CNV (genes) - QVALUE: Q-value of the CNV (qvalue) - OLAPAFIMGAG: Overlap with inhouse database of IMGAG and GnomAD (overlap afgenomesimgag) - CNPATO: Known pathogenic CNVs (cnpathogenic) - CLINVAR: ClinVar overlapping CNVs (clinvarcnvs) - GENEINFO: Gene informations (i.e. stringency, region, etc.) (geneinfo) - IHPATO: Known CNVs in inhouse database (ngsdpathogeniccnvs)

Usage

  • -r REFERENCE, --reference REFERENCE reference genome in FASTA format.
  • -i INPUT [INPUT ...], --input INPUT [INPUT ...] input file(s) in ClinCNV TSV format.
  • -s SAMPLEID [SAMPLEID ...], --sampleid SAMPLEID [SAMPLEID ...] sample id(s). Will be infered from input filename if not given.
  • -c CONFIDENCEINTERVAL, --confidenceinterval CONFIDENCEINTERVAL confidence interval around POS/END for imprecise variants. Will be used in in both directions. Defaults to 500 resulting in CIPOS=-500,500;CIEND=-500,500.

Attribution

  • Uses pyfaidx (see Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. 2015. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e970v1 https://doi.org/10.7287/peerj.preprints.970v1)

Owner

  • Name: Institut für Humangenetik - Medizinische Hochschule Hannover
  • Login: MHH-Humangenetik
  • Kind: organization
  • Location: Germany

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: CNV2VCF
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Benedikt
    family-names: Schnur
    email: schnur.benedikt@mh-hannover.de
    affiliation: Hanover Medical School (MHH)
    orcid: 'https://orcid.org/0000-0002-1977-7878'
identifiers:
  - type: doi
    value: 10.5281/zenodo.7733351
abstract: >-
  CNV2VCF is a tool to convert output of ClinCNV to VCF
  format.
license: MIT

GitHub Events

Total
  • Issue comment event: 3
  • Push event: 5
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issue comment event: 3
  • Push event: 5
  • Pull request event: 1
  • Create event: 1

Dependencies

.github/workflows/build_latest.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v3 composite
Pipfile pypi
  • bandit * develop
  • black * develop
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  • pytest * develop
  • pytest-cov * develop
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  • openpyxl *
  • pandas *
  • pyfaidx *
Pipfile.lock pypi
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  • python-dateutil ==2.8.2
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pyproject.toml pypi