A pipeline to find allelic ratios in regions of clone-specific LOH in 10X scRNA-seq data. This uses a modified version of the scAlleleCount script.
snvworkflow, edit config.yaml with the required files. Briefly, you'll need:
- A BAM file from CellRanger of the scRNAseq
- A tsv file with sites of germline heterozygous SNPs
- A csv file detailing clone specific copy number regions
Dockerfile is a template for creating a Docker container with all required software.