https://github.com/alexcoppe/pythonvcf
https://github.com/alexcoppe/pythonvcf
Last synced: 5 days ago
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- Host: GitHub
- URL: https://github.com/alexcoppe/pythonvcf
- Owner: alexcoppe
- License: mit
- Created: 2021-12-10T16:57:32.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-03-17T15:10:32.000Z (about 1 year ago)
- Last Synced: 2024-03-18T05:06:24.324Z (about 1 year ago)
- Language: Python
- Size: 63.5 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pythonvcf :dna:
A Python package and a set of script for working with VCFs files.
# Available scripts :man_technologist:
| Script | Description|
| ------------- |:-------------|
| parse_clinvar_vcf.py | Creates a tab separated file from the VCF used as input |
| update_clinvar_in_vcf.py | Updates a VCF file annotated with [ANNOVAR](https://annovar.openbioinformatics.org/en/latest/) using a [SQLite](https://www.sqlite.org/index.html) made from the table produced by parse_clinvar_vcf.py script |
## :snake: filter_vcf_by_clinvar_stars.py
A script that filters a VCF file based on ClinVar [gold stars](https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/). It needs the VCF to filter, the VCF downloaded from [ClinVar](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/).
Option | Long Option | What does it do
------------ | ------------- | -------------
-h | --help | Show help
-v | --vcf | The vcf to be filtered
-c | --clinvar | The vcf from ClinVar
-s | --stars | The minimum number of stars to keep
##### Example
```console
>>> filter_vcf_by_clinvar_stars.py -v your_vcf.vcf -c clinvar.vcf -s 3
```
## :snake: filter_vcf_by_bed.py
This script filters a VCF by using a BED file. It needs the VCF to be filtered and the [.BED](https://en.wikipedia.org/wiki/BED_(file_format)) file with the rangers you want to filter.
Option | Long Option | What does it do
------------ | ------------- | -------------
-h | --help | Show help
-v | --vcf | The VCF to be filtered
-b | --bed | The BED used as filter
##### Example
```console
>>> filter_vcf_by_bed.py -v your_vcf.vcf -b your.bed
```
## Installation
pip install -e ./
## Uninstallation
- pip uninstall pythonvcf.py
- rm -rf scripts/pythonvcf.py.egg-info/