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Frequently Asked Questions
==========================

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:large:`How is pVACtools licensed?`

pVACtools is licensed under `BSD 3-Clause Clear License
<https://spdx.org/licenses/BSD-3-Clause-Clear.html>`_.

:large:`Where can I get help?`

Bug reports or feature requests can be submitted on the `pVACtools Github page <https://github.com/griffithlab/pVACtools/issues>`_. You may also contact us by email at help@pvactools.org.

:large:`How do I cite pVACtools?`

Jasreet Hundal+, Susanna Kiwala+, Joshua McMichael, Christopher A Miller,
Alexander T Wollam, Huiming Xia, Connor J Liu, Sidi Zhao, Yang-Yang Feng,
Aaron P Graubert, Amber Z Wollam, Jonas Neichin, Megan Neveau, Jason Walker,
William E Gillanders, Elaine R Mardis, Obi L Griffith, Malachi Griffith.
`pVACtools: a computational toolkit to select and visualize cancer
neoantigens <https://doi.org/10.1101/501817>`_.
bioRxiv 501817; doi: https://doi.org/10.1101/501817. (+)equal contribution.

Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, 
William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, 
and Malachi Griffith. `Accounting for proximal variants improves neoantigen prediction <https://www.nature.com/articles/s41588-018-0283-9>`_. 
Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: `30510237 <https://www.ncbi.nlm.nih.gov/pubmed/30510237>`_.

Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi
L. Griffith, Elaine R. Mardis, and Malachi Griffith. `pVACseq: A genome-guided
in silico approach to identifying tumor neoantigens <http://www.genomemedicine.com/content/8/1/11>`_. Genome Medicine. 2016,
8:11, DOI: 10.1186/s13073-016-0264-5. PMID: `26825632
<http://www.ncbi.nlm.nih.gov/pubmed/26825632>`_.