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MarkIlluminaAdapters missing from GATK pipelines

The best practices GATK exome and genome pipelines seem to not perform adapter clipping/marking with MarkIlluminaAdapters as described here: https://software.broadinstitute.org/gatk/documentation/article?id=6483

This would likely lead to significant issues in subsequent alignments and false positive calls.

Why is MarkIlluminaAdapters not part of the standard GATK pipelines even though the GATK website says it should be?

Answers

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