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BQSR on individual samples?
I have sequenced each of my samples with a single library and would like to recalibrate my bams. I have a merged (with a @RG tag for each sample) bam and the original single-sample bams.
I ran BaseRecalibrator on each sample bam because running on the merged was slow. My question is, is running BaseRecalibrator independently on each sample bam the same as running it on a merged bam where each readgroup corresponds to a single sample?