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.
Note that development happens on the dev branch to manage versions. The master branch is the legacy version of snpeffr maintained for backwards compatibility with older versions of mycosnp-nf.
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@dev")
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/dev.zip")
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
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
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
- 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.)
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