snvworkflow

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.

Usage

To run 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

The Dockerfile is a template for creating a Docker container with all required software.