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Is it possible to have a much smaller bam output from PrintReads?
I am using 3.3-0. The size of recalibrated bam is about two times the size of indel realigned bam. I tried adding the -s flag to PrintReads but the output becomes 5% smaller only.
Still, 5% smaller is still too big for me. I usually keep the recalibrated bam for igv visualization. Is it possible to make its size closer to the indel realignment bam without sacrificing the accuracy of downstream analysis and also visualization in igv???