Clonal hematopoiesis in metastatic urologic malignacies

This repo contains the relevant snakemake rules for to carry out FastQ modification, BAM generation and variant calling as explained in our article "Clonal hematopoiesis in metastatic urothelial and kidney cancer".

Pre-requisites

Our analysis pipeline is written in Python using the Snakemake workflow management system. Please follow these instructions for setup:

1. All dependencies needed to run the pipeline are provided in the envs/snakemake.yaml file. You can create the snakemake environment by running conda env create -f snakemake.yaml
2. GATK's base calibration tool that we use requires the following three files (resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf, resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf, resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf) which can be downloaded from this Google Cloud link.
3. Mutect2 requires a panel of normals, which can be obtained from this link.

Running the workflow

1. Edit the config.yaml file with the file locations of relevant files and directories.
2. Workflow expects raw FastQ files to be placed into the results/data/fastq directory. All files placed here will be processed by the pipeline.
3. The pipeline can be evoked with the snakemake command. By issuing snakemake -n you can issue a dry run.