• sc_snp.smk (Required): Snakemake workflow file.
• sc-snp-demux.yml (Required): The conda environment yml file. Is used by the Snakemake workflow to install all required packages
• config.yml (Required): Input configuration specifying 3 important parameters:
  1. The path to the 10X output folder. Must contain "possorted_genome_bam.bam" and "filtered_feature_bc_matrix"
  2. The path to the directory containing the reference SNPs
  3. The VCF file name. We used 'genome1K.phase3.SNP_AF5e2.chr1toX.hg38' from the 1000 genome project.
• sc_snp_scaling.sh: Example slurm script calling the Snakemake workflow on some samples

To perform SNP-calling and demultiplexing on the pooled samples, cellsnp-lite is first used to call SNPs on a cell-level using the 1000 genomes-based reference variant call file for hg38 at a resolution of 7.4 million SNPs. SNPs with <20 counts and a <10% minor allele frequency were filtered out, as per the developer recommendations. Finally, the tool vireo is called on the outputs from cellSNP-lite to demultiplex the pooled data using the cellsnp-lite-derived genotype information.