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Getting StartedΒΆ

pVACseq provides a set of example data to show the expected input and output files. You can download the data set by running the pvacseq download_example_data command.

The example data output can be reproduced by running the following command:

pvacseq run \
<example_data_dir>/input.vcf \
Test \
HLA-G*01:09,HLA-E*01:01,H2-IAb \
NetMHC PickPocket NNalign <output_dir> \
-e 9,10 \
-i <example_data_dir>/additional_input_file_list.yaml --tdna-vaf 20 \
--net-chop-method cterm --netmhc-stab \
--top-score-metric=lowest -d full --keep-tmp-files

A detailed description of all command options can be found on the Usage page.