# 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
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
1 maintainer
Metadata
1 maintainer
Release files for seq-dove 0.2.1
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| seq_dove-0.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Release files / seq_dove-0.2.1-py3-none-any.whl
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| Tags | Python 3 |
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