SNP-masked refererence genome

Create a reference genome sequence with "injected" SNPs/SNVs from other mouse strains.

Input files

• mouse reference genome
• mouse annotation (GTF)
• SNP file

Dependencies

The snpsplit tool is defined in a conda environment in workflow/envs/snpslit.yml.

CellRanger is proprietary software and cannot be installed via Conda. It needs to be manually downloaded and the path to its executable stored in workflow/config.yaml.

On the DKFZ Compute Cluster Cellranger is installed as module and available at: /software/cellranger/6.0.0/bin/cellranger mkref

Configuration

The configuration in workflow/config.yaml contains:

• path to reference genome
• path to gene annotation
• path to cellranger mkref
• list of Strains from the mouse genome project (MGP)

Run

The workflow can be run by executing:

snakemake -c1 --configfile config.yaml --use-conda

To use the LSF job scheduler on the DKFZ cluster run with

snakemake --cluster "bsub -n4 -q verylong -R rusage[mem=100GB]" -p -j2 -c4 --configfile config.yaml --use-conda

Output files

Output files of the workflow are stored in the subdirectory output/

TO DO

• Add a download function for the SNP data from ftp.sanger.ac.uk/pub/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz This is currently not activated due to proxy issues in the DKFZ working.