pvacfuse的使用

pvacfuse是pvactools的一个工作组件，用来预测融合基因中的新抗原。

Prerequisites（准备工作）

Fusion detection and annotation（融合基因检测和注释）

pvacfuse需要准备bedpe文件，带有融合基因注释信息。Fusion detection will be preformed using INTEGRATE with annotations from INTEGRATE-Neo. It should be possible to start with fusions from another caller, convert the output to bedpe format, annotate the bedpe with INTEGRATE-Neo and then feed these candidates into pVACfuse.

Getting Started

示例数据下载，准备

Download Example Data

usage:

pvacfuse download_example_data [-h] \home\gml\work\test

List Valid Alleles

usage:

pvacfuse valid_alleles [-h] [-p {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}]

从{ }中选择一种算法即可，用参数-p来指定算法。

List Allele-Specific Cutoffs

usage:

pvacfuse allele_specific_cutoffs [-h] [-a ALLELE]

pvacfuse 运行

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

pvacfuse run \
<example_data_dir>/fusions.bedpe.annot \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e 8,9,10

根据自己的数据存储目录，修改如下：

pvacfuse run \
/home/gml/work/test/pvacfuse_example_data/fusions.bedpe.annot \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
/home/gml/work/test/pvacfuse_result/ \
-e 8,9,10

运行以上程序就会得到所需要的结果。