Snakemake based python script of verifybamID that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples and it can detect sample contamination.
- load Anaconda or Install anaconda
- conda create --name verify-env
- source activate verify-env
- conda install -c bioconda verifybamid
- conda install -c bioconda samtools
To Run the script on cluster using this command 'modify cluster.json parameters according to your cluster configuration
snakemake -j 999 --configfile config.yaml --use-conda --nolock --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -c {cluster.ncpus} -n {cluster.ntasks} -t {cluster.time} --mem {cluster.mem}"