I'm working with NovaSeq data for WGS and, as Terra expects an ubam input for some pipelines, converting illuminas' bcl straight to ubam makes the process computationally cheaper and faster. This option is discussed on GATK's forum https://software.broadinstitute.org/gatk/documentation/article?id=6483, saying that a specific tutorial was to be developed (#6570). However, afaik, this tutorial was never developed.
I'm wondering if there is a special reason for this (you figured out it was a bad idea after some experimentation) and there is a better solution for that, or it was just lack of time.
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