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What intermediate file to keep, and what to delete?
I am running an RNA-seq project, and per Best Practices I at least have the following intermediate files:
1. BAMs after MarkDuplicates,
2. The output of SplitNCigarReads using (1) as input,
3. BQSR tables, one per sample each pass, and
4. The BAM file after applying the second-pass BQSR table.
My institution's storage is extremely limited, and I'd need to delete some of these files. Which of these, you think, should I keep? Personally I would keep the last one at least, since both HaplotypeCaller and MuTect2 would take that as input, but what else?