How to cite
===========

GREEN-DB
~~~~~~~~
If you use any information from GREEN-DB please cite:
`GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing <https://www.biorxiv.org/content/10.1101/2020.09.17.301960v1>`_
Giacopuzzi E., Popitsch N., Taylor JC. BiorXiv (2020)

GREEN-VARAN
~~~~~~~~~~~
When you use greenvaran for annotation please cite

|   `GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing <https://www.biorxiv.org/content/10.1101/2020.09.17.301960v1>`_
|    Giacopuzzi E., Popitsch N., Taylor JC. BiorXiv (2021)

If you use the GREEN-VARAN Nextflow workflow for additional annotations also cite

|   `Vcfanno: fast, flexible annotation of genetic variants <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5>`_ 
|    Brent S. Pedersen, Ryan M. Layer & Aaron R. Quinlan. Genome Biology volume 17, Article number: 118 (2016)

If you include annotation with a prediction score please also cite the corresponding paper

.. csv-table::
    :header: "Score","PUBMED ID"
    :widths: 20,20

    CADD,30371827
    DANN,25338716
    EIGEN,26727659
    ExPecto,30013180
    FATHMM-MKL,25583119
    FATHMM-XF,28968714
    FINSURF,doi.org/10.1101/2021.05.03.442347
    FIRE,28961785
    GenoCanyon,26015273
    GenoSkyline-plus,27058395
    GWAVA,24487584
    LinSight,28288115
    NCBoost,30744685
    ncER,31748530
    ReMM,27569544

Population AF
~~~~~~~~~~~~~
If you use population AF annotation with GREEN-VARAN workflow also cite the gnomAD paper:
`The mutational constraint spectrum quantified from variation in 141,456 humans <https://www.nature.com/articles/s41586-020-2308-7>`_