Metadata-Version: 2.0
Name: seq-dove
Version: 0.2.6
Summary: Set of tools for downstream vcf analysis
Home-page: UNKNOWN
Author: bars
Author-email: barslmn@gmail.com
License: UNKNOWN
Keywords: genomics next generation sequencing variant discovery human genetics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Dist: pandas
Requires-Dist: responses

# Dove
Variant analysis tool kit written in python3 for downstream vcf analysis.

## Online Variant Anotation
Annotates given vcf file using Ensembl VEP API.

## Multi Genome Analysis
Filters index sample's variants with parents and siblings based on given inheritance pattern.

## Variant Filter
Filters annotation file by given parameters.

## Quick Install
* Linux&Mac  
> sudo pip3 install --index-url https://test.pypi.org/simple/ dove
* Windows
> pip install --index-url https://test.pypi.org/simple/ dove

## Example Uses

* OVA examples  
>  dove OVA -i input.vcf -o output.csv

* MGA examples  
>  dove MGA -i index.csv -m mother.csv -f father.csv -a trio -p AR -o output.csv
>  dove MGA -d pedigree.csv -a siblings -o output.csv

* VF generic filter examples
>  dove VF -i index.csv -z 1/1 -f 0.01 -r 20 -b protein_coding -o output.csv

* VF Specific filter examples
>  dove VF -t filterfile.txt

* dove examplefile
>  dove examplefile --help
>  dove examplefile -e both

* dove updateomim
>  dove updateomim --help
>  dove updateomim -k apikey


