pvacVector的使用

pVACvector is designed to aid specifically in the construction of DNA vector based personalized cancer vaccines. It takes as input either a pVACseq output tsv file or a fasta file containing peptide sequences and returns a peptide ordering that minimizes the effects of junctional epitopes (that may create novel peptides) between the sequences.
pVACvector旨在帮助专门构建基于DNA载体的个性化癌症疫苗。它将pVACseq输出tsv文件或含有肽序列的fasta文件作为输入，并返回肽序列，其最小化序列之间的连接表位（可能产生新的肽）的影响。

Prerequisites

There are two options for the input file when running the pVACvector tool:

A fasta file

This file contains protein sequences of candidate neoepitopes to use for vector design.

A pVACseq output TSV

This file has been filtered to include only the neoepitopes to use for vector design. If this file type is used, it is also necessary to provide the original VCF used in the pVACseq run via the --input_vcf option. Output TSVs from MHC Class I and Class II pVACseq results can be combined into one by concatenating the two files and removing the duplicate header line.

Note: Note that if you supply a fasta file of peptides, these peptides will be used directly in the analysis and used in the final output. However, if you use a pvacseq TSV and variants VCF then the length of peptides extracted for junctional epitope testing and reporting in your output will be determined by the --input-n-mer option.

Getting Started

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

准备数据

Download Example Data

pvacfuse download_example_data [-h] destination_directory

本地命令如下：

pvacvector download_example_data [-h] /home/gml/work/test

List Valid Alleles

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

本地命令如下：

 pvacvector valid_alleles -p MHCflurry

List Allele-Specific Cutoffs

pvacvector allele_specific_cutoffs  [-h]  [-a ALLELE]

本地：

pvacvector allele_specific_cutoffs -a ALLELE

Usage

There are two option as to how to run pVACvector depending on the input file type used. You can either use a pVACseq output TSV of neoepitopes or a FASTA file of peptide sequences.

Run pVACvector with a pVACseq output TSV

command:

pvacvector run \
<example_data_dir>/input.tsv \
Test \
H-2-Kb \
NetMHC \
<output_dir> \
-e 8 \
-v <example_data_dir>/input.vcf
--keep-tmp-files

本地命令如下：

pvacvector run \
/home/gml/work/test/pvacvector_example_data/input.tsv \
Test \
H-2-Kb \
NetMHC \
/home/gml/work/test/pvacvector_result \
-e 8 \
-v /home/gml/work/test/pvacvector_example_data/input.vcf \
--keep-tmp-files

Run with an input FASTA file

pvacvector run \
<example_data_dir>/input.fa \
Test \
H-2-Kb \
NetMHC \
<output_dir> \
-e 8 \
--keep-tmp-files

本地命令如下：

pvacvector run \
/home/gml/work/test/pvacvector_example_data/input.fa \
Test \
H-2-Kb \
NetMHC \
/home/gml/work/test/pvacvector_result \
-e 8 \
--keep-tmp-files

运行均成功。