A snakemake to downsample reads from a bam file, following GATK best practices.
This repository contains all the folders needed to run the snakemake. logs/cluster/ currently contains a placeholder file because GitHub does not allow empty folders, but after copying this repository structure to the server, this placeholder file can be removed from the server.
To run:
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update config/samples.yaml and config/config.yaml as per the directions in those files
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load all modules listed in downsampling_bam_paired.snakefile
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verify all paths are correct for your application
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launch snakemake from directory containing the snakemake file with command referenced downsampling_bam_paired.snakefile (with -np) for a dry run which will look for errors and list out all necessary jobs. If no errors and jobs look correct
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relaunch snakemake with command referenced in downsampling_bam_paired.snakefile without -np
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snakemake steps will be launched as jobs to the cluster at the Fred Hutchinson Cancer Research Center.