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Is it still valid to pre-process read groups separatedly when multiplexing?
I have 60 DNA samples, each one was barcoded, then pooled (10 samples per pool), and each pool was sequenced in 9 different lanes. So for each sampel I have 9*2(PE)=18 FASTQ files. In total, 1080 FASTQs.
My intension is to do variant calling using haplotype caller.
My intention is to follow the recomendations found in this tutorial https://gatkforums.broadinstitute.org/gatk/discussion/3060/how-should-i-pre-process-data-from-multiplexed-sequencing-and-multi-library-designs
However, I have been suggested that this might not be the most up to date reference workflow, and that is more convenient to merge all BAMs right after alignment as one read group, given that there are no lane derived artifacts.
My question is: is the tutorial still valid? (valid = still used by the community and at broad)
Thanks in advance!