Getting Started

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>/HCC1395.splice_junctions.tsv \
HCC1395_TUMOR_DNA \
HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
all \
<output_dir> \
<example_data_dir>/annotated.expression.vcf.gz \
<example_data_dir>/ref_genome.fa \
<example_data_dir>/Homo_sapiens.GRCh38.105.chr.gtf.gz \
-e1 8,9,10 \
-e2 15 \
--normal-sample-name HCC1395_NORMAL_DNA

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