RedfishAmpliconPipe

A snakemake pipeline for processing and snp calling of amplicon data for redfish species identification.

Setup / Installation

The easiest way to set up the snakemake environment is with conda. The commands below should help you get started, but exact setup may vary depending on your environment.

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# build the conda env
conda install -n base -c conda-forge mamba
conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake

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# activate the snakemake env
conda activate snakemake

pip install pysam
pip install matplotlib

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# configure the channels and install the binf packages needed (into the snakemake environment)
conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge

# install the necessary software (not in the channels above)
conda install fastp
conda install plink

On subsequent executions you can simply run the following to activate the snakemake env

conda activate snakemake

Pipeline

Setup the workflow

Once inputs are provided, we build a config file

python redfish_snake_setup.py 

The pipeline is currently broken up into two snakemake workflow files, so as to delimit the two components (and logical end points of the workflow). The first workflow, RedfishMarkerCall, will take the data from raw fq files to variants called and stored in vcf format. The second workflow, PlinkSnakefile takes the output vcf from the previous workflow and conducts filtering and conversion in plink to produce a ped/map file pair for use with subsequent data analysis.

Commands for execution of Amplicon calling Snakemake workflow

#execute the snakemake file

#dry run to test procedure
snakemake --snakefile RedfishMarkerCall -np

#make a diagram of the process
snakemake --dag  | dot -Tsvg > redfish_pipeline.svg #make a diagram of it

# run the whole pipeline
snakemake --cores

# run specific rules
snakemake -R fastp_cut -n #-n makes it a dry run

Individual steps listed below:

snakemake --snakefile RedfishMarkerCall -R fastp_cut 
snakemake --snakefile RedfishMarkerCall -R bwa_index 
snakemake --snakefile RedfishMarkerCall -R bwa_map
snakemake --snakefile RedfishMarkerCall -R samtools_sort
snakemake --snakefile RedfishMarkerCall -R samtools_index
snakemake --snakefile RedfishMarkerCall -R bcftools_call
snakemake --snakefile RedfishMarkerCall -R variant_filter

Commands for execution of Plink conversion Snakemake workflow

The second step is a simple series of plink commands to go from a vcf format to a filtered ped/map genotype data file pair

#execute the snakemake file

#dry run to test procedure
snakemake --snakefile PlinkSnakefile -np

snakemake --snakefile PlinkSnakefile --cores

Tests

There are five example files and the reference panel included within the data/ folder. These allows for a small test run of the pipeline to be conducted.