pVACsplice provides a set of example data to show the expected format of input and output files. You can download the data set by running the pvacsplice download_example_data command.
The example data output can be reproduced by running the following command:
pvacsplice run \
<example_data_dir>/input_junctions.tsv \
<sample_name> \
HLA-A*01:01,HLA-A*02:01,HLA-B*15:01,HLA-B*57:01,HLA-C*03:03,HLA-C*06:02 \
all_class_i \
<output_dir> \
annotated_variants.vcf \
ref.fa
A detailed description of all command options can be found on the following page.