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The goal of the snpeffr package is to filter and parse outputs generated by snpeffr for MDB/Fungi Net.It depends on the R packagesdata.table andR.utils. If using the command linescript included, you will also need the packagedocopt.

Note that development happens on the dev branch to manage versions. The master branch is the legacy version of snpeffr maintained for backwards compatibility witholder versions ofmycosnp-nf.

You can install the development version of snpeffr like so:

# if remotes not installed, then install the pkgif(!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 gitremotes::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 examplevcf_exe <- file.path(path.package("snpeffr"), "vcf-filter_ann_mod.vcf.gz")# basic exampleout <- 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 atinst/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 interestUsage:    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=221637:221663,fks1_hs2=223782:223805,fks1_hs3=221805:221807]    -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 snpeffrhere, 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

• Usesnpsift to do some of the upstream filtering (should be faster than reading in thelarger vcf using data.table, currently only the split command is a module, so we wouldneed to set up the filter command as a module if we wanted to use this.)

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