Pipeline gets assembly in fasta format, and reads in fq format as default (see Required settings section below).
As an output it generates hetero/homozygosity plots, coverage plots considering PAR (Pseudoautosomal regions).
All general results you can find in data_output folder.
All additional information can also be found in readme files incide required directories.
cd <pipeline_working_dir>
git clone https://github.com/BioHappyThreeFriends/varcaller.git
cd varcaller
It is recommended to create a fresh conda environment using mamba or conda.
mamba env create --name varcaller --file ./environment.yaml
# or:
# conda env create --name varcaller --file ./environment.yaml
Activate conda environment with snakemake:
conda activate varcaller
snakemake --cores 32 --configfile config/config.yaml --forceall --use-conda --profile profile/slurm/ --printshellcmds --latency-wait 60
