https://github.com/kubranarci/vcftodata
a python package using pysam to parse VCF file to simple table formats
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (5.7%) to scientific vocabulary
Repository
a python package using pysam to parse VCF file to simple table formats
Basic Info
- Host: GitHub
- Owner: kubranarci
- License: mit
- Language: Python
- Default Branch: main
- Size: 35.2 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
VcfToData
VcfToData is a Python tool for converting VCF files into table format (TSV or CSV) with additional annotations such as GNOMAD allele frequency and customizable INFO/FORMAT fields.
Installation
To install VcfToData, clone the repository and install the required dependencies:
```bash git clone https://github.com/kubranarci/VcfToData.git cd VcfToData pip install -e .
```
Usage
vcf-to-data --vcf
Options
--vcf: The input VCF file.
--out: Output prefix.
--output-format: The format of the output file - csv, tab or json
--gene-list: Optional file with a list of genes to annotate.
--gnomad-af: Optional GNOMAD_AF file for allele frequency data.
--info-fields: Space-separated list of INFO fields to extract (e.g., RankScore, Annotation).
--format-fields: Space-separated list of FORMAT fields to extract (e.g., GT, DB).
Owner
- Name: Kübra Narcı
- Login: kubranarci
- Kind: user
- Location: Heidelberg
- Company: @ghga-de @DKFZ-ODCF
- Twitter: kubranarci
- Repositories: 3
- Profile: https://github.com/kubranarci
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