Snakemake User Guide

We added an additional snakemake mini-pipeline to call SVs from bam using Sniffles2, cuteSV and SVIM.

To use snakemake to detect SVs:

0, Prepare environments

 conda create -n svim_env --channel bioconda svim

 conda install sniffles=2.5.3
 
conda install -c bioconda cutesv

1, Modify the config.yml file

# Folder where all the outputs are saved
BASE_OUTPUT_DIR: example_outputdir
#Modify: example_outputdir to your output directionary
# Folder where input bam and index file are saved and filename
BASE_INPUT_DIR: example_inputdir/input.bam
# Folder where reference file saved and filename
BASE_REF_DIR: example_refdir/GRch38.fa
# Parameter for analysis
THREADS: number of threads ###note that SVIM could not run on multi-threading

2, Run the process

snakemake -s work_flow.snakefile --configfile config.yml