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

🐛 If you are sure you have found a bug, please submit a bug report. You can submit your bug reports on Github here

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.