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Mutant peptide ranking for personalized cancer vaccines

Project description

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# vaxrank

Selection of mutated protein fragments for therapeutic personalized cancer vaccines.

## Usage


vaxrank \
--vcf test/data/b16.f10/b16.vcf \
--bam test/data/b16.f10/b16.combined.bam \
--vaccine-peptide-length 25 \
--mhc-predictor netmhc \
--mhc-alleles H2-Kb,H2-Db \
--padding-around-mutation 5 \
--output-ascii-report vaccine-peptides.txt \
--output-pdf-report vaccine-peptides.pdf \
--output-html-report vaccine-peptides.html

## Installation

Vaxrank can be installed using [pip](

pip install vaxrank

Note: to generate PDF reports, you first need to install [wkhtmltopdf](, which you can do (on OS X) like so:

brew install Caskroom/cask/wkhtmltopdf

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