PeptoVar

PeptoVar - Peptides of Variations

Overview

PeptoVar is a program for annotation of genomic variants in protein coding genes and generation of variant peptides.

• Annotation of variants:
  • comprehensive information of potential compound effects of combining alternate alleles across multiple variant loci
• Annotation of peptides:
  • variant peptides of a population
  • personalized peptidome for a sample (phased and unphased data can be used)
  • unique peptides for a pair of samples

The PeptoVar annotation for human peptides is accessible online as PeptoVarDB: http://www.peptovar.online.

The PeptoVar project was supported by RFBR, project number 17-04-02186.

Requirements

• Linux or MacOS
• python >= 3.5
• pysam module >= 0.11.2.2

Installation

• install pysam package using pip:

  pip3 install pysam

• download latest stable PeptoVar build from this page
• unzip the archive
• add resulting folder to your PATH variable
  • or add symbolic link for PeptoVar script to your bin folder
  • or use PeptoVar directly by specifying full path to the executable script

Examples of usage

Annotation of variations

The example of annotation of genomic variations in the protein coding regions:

PeptoVar.py -var nonsyn -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar.py -var nonsyn -indir ./testdata

Peptides for combinations of variations in the set

This example illustrates usage virtual sample with all variations:

PeptoVar.py -peptlen 9 10 11 -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar.py -peptlen 9 10 11 -indir ./testdata

Peptides for a sample

This example illustrates usage for sample SAMPLE01:

PeptoVar.py -samples SAMPLE01 -peptlen 9 -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar.py -samples SAMPLE01 -peptlen 9 -indir ./testdata

Unique peptides for a pair of samples

This example illustrates usage for the pair of samples: SAMPLE01 and SAMPLE02:

PeptoVar.py -samples SAMPLE01 SAMPLE02 -peptlen 9 -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar.py -samples SAMPLE01 SAMPLE02 -peptlen 9 -indir ./testdata

Documentation

Detailed PeptoVar description can be found in the manual

If you haven’t found the answer to your question in the docs, or have any suggestions concerning new features, feel free to create an issue here, on GitHub, or write an email to dmitry.malko at gmail.com:

License

Copyright (c) 2017, 2018, D. Malko All Rights Reserved

PeptoVar is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.