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I have read on your recent slides for "Data Compression with Reduce Reads" that "Tumor and Normal samples (or any set of samples) get co-‐reduced, meaning that every variable region triggered by one sample will be forced in every sample."
I have data from 4 variant strains of an organism, my samples in RG info, and 4 individuals for each strain, my libraries in RG info. Currently I have a bam file for each of the 16 different libraries.
If I want to run ReduceReads as I have quite high coverage, but preserve information across all of my samples where a site is not consensus in just one as there is no snp information available for this organism and I don't want to lose any important data. Should I merge all bam files for all samples before proceeding with ReduceReads with downsampling turned off? Or just leave out ReduceReads?