barslmn / dove

DOwnstream Vcf Evaluation

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