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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