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README.md

snvworkflow

DOI

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.

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