https://github.com/hammerlab/vaxrank
Tip revision: 23fe92f5dae04ead2d5d2df0231855eea1921926 authored by Alex Rubinsteyn on 19 August 2020, 19:40:48 UTC
Merge pull request #191 from openvax/use-isovar-for-all-variant-counts
Merge pull request #191 from openvax/use-isovar-for-all-variant-counts
Tip revision: 23fe92f
run-vaxrank-b16-test-data.sh
vaxrank \
--download-reference-genome-data \
--vcf test/data/b16.f10/b16.vcf \
--bam test/data/b16.f10/b16.combined.bam \
--vaccine-peptide-length 15 \
--mhc-predictor netmhc \
--mhc-alleles H2-Kb,H2-Db \
--mhc-epitope-lengths 8 \
--padding-around-mutation 0 \
--min-epitope-score 10e-100 \
--num-epitopes-per-peptide 5 \
--output-ascii-report vaccine-peptides-report.txt \
--output-html-report vaccine-peptides-report.html \
--output-pdf-report vaccine-peptides-report.pdf \
--output-xlsx-report vaccine-peptides-report.xlsx \
--output-neoepitope-report neoepitope-report.xlsx \
--output-json-file vaccine-peptides-report.json \
--output-csv vaccine-peptides.csv \
--output-passing-variants-csv vaccine-peptides-all-passing.csv \
--output-reviewed-by "John Doe,Jane Doe" \
--output-final-review "All the Does" \
--output-patient-id "Test Patient"