snpeffr

The goal of the snpeffr package is to filter and parse outputs generated by snpeffr for MDB/Fungi Net. It depends on the R packages data.table and R.utils. If using the command line script included, you will also need the package docopt.

Installation

You can install the development version of snpeffr like so:

# if remotes not installed, then install the pkg
if(!require(remotes)) install.packages("remotes")

remotes::install_github("CDCgov/snpeffr")

Or if you don't have git set up:

# install from zip location so no need for git
remotes::install_url("https://github.com/CDCgov/snpeffr/archive/refs/heads/master.zip")   

Example

You can test out the function on the example data provided:

library(snpeffr)

# path to example vcf included in package 
# replace with path to your vcf output if running on your own example
vcf_exe <- file.path(path.package("snpeffr"), "vcf-filter_ann_mod.vcf.gz")

# basic example
out <- snpeffr(vcf_path = vcf_exe)

head(out)

# to see function documentation/help for more details on the arguments and output
?snpeffr

Command-line script

You can also use a command line version of this script at inst/snpeffr.R.

Download the file and from the directory where it's downloaded, run:

./snpeffr.R -f path_to_vcf

To get help and options for the command line version:

./snpeffr.R -h

Which will display the following help message:

Parse snpeff output to summary of mutations at positions of interest

Usage:
    snpeffr.r [--fpath=FPATH] [--pos=POS] [--genes=GENES] [-exc=EXCL] [-out=OUT]

Options:
    -v, --version           Show version.
    -f FPATH --fpath=FPATH  path to input vcf file from snpeff
    -p POS --pos=POS        format as named comma separated list
                            of positions (no spaces), i.e. see default
                            [default: fks1_hs1=221638:221665,fks1_hs2=223782:223805]
    -g GENES --genes=GENES  a list of comma separated gene names (no spaces) [default: CAB11_002014]
    -e EXCL --exc=EXCL      a quoted regular expression for effects to exclude [default: 'synonymous_variant']
    -o OUT --out=OUT        csv or gz file to save output to [default: out.csv]
    -h, --help              show this help text

To set it up to run from anywhere in your environment, add the path to your .bashrc file:

export PATH=$PATH:path/to/snpeffr.R

Docker image

There is a docker image to run snpeffr here, built off of rocker/r-ver. It moves the command line script to the top level. To run inside docker use:

# and other associated commands
./snpeffr.R -h

Next steps

• Finalize output schema:
  • keeping in the sequence of the mutation as well as the protein change?
  • filtering to ones that only have hgvs.p annotation or keeping all?
  • adding in column for putative impact per snpeff?
• Use snpsift to do some of the upstream filtering (should be faster than reading in the larger vcf using data.table, currently only the split command is a module, so we would need to set up the filter command as a module if we wanted to use this.)
• Set up as a nextflow module that can be implemented downstream from the snpeff module once it is added to mycosnp-nf.

CDCgov GitHub Organization Open Source Project

General disclaimer This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.

Related documents

• Open Practices
• Rules of Behavior
• Thanks and Acknowledgements
• Disclaimer
• Contribution Notice
• Code of Conduct

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This source code in this repository 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 Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

Privacy Standard Notice

This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.

Contributing Standard Notice

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records Management Standard Notice

This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.

Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.