ANVAGE
ANnotation Variants GEnome is a toolkit software to perform routine operations that involve VCF, GFF3 and FASTA genome files.
Installation
pip3 install anvage
Quick start
anvage select --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--annotation tests/data/genome.gff3 \
--selectionAnnotationType CDS \
--output_prefix res
anvage synonymous --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--annotation tests/data/genome.gff3 \
--output_prefix res
anvage flank --vcf tests/data/sample.vcf \
--genome tests/data/genome.fasta \
--windowsSize 25 \
--output_prefix res
Credits
ANVAGE was coded and written by Emilie Boulanger and Pierre-Edouard Guerin.
We thank the following people for their help in the development of this software: Stephanie Manel, Laura Benestan.
The CNRS research unit CEFE, team Biogeography of Vertebrates supports and contributes to the ANVAGE project.
Contributions and Support
Citations
You can cite the ANVAGE publication as follows:
Climate differently influences the genomic patterns of two sympatric marine fish species
Emilie Boulanger, Laura Benestan, Pierre-Edouard Guerin, Alicia Dalongeville, David Mouillot, Stéphanie Manel
Journal of Animal Ecology. 2021 Oct 31. DOI: 10.1111/1365-2656.13623
License
ANVAGE is licensed under MIT License. Please see the LICENSE file.