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If I need to use SetNmMdAndUqTags?
I want to do snp calling and I have used MergeBamAlignment to merge ubam and bam files together with SORT_ORDER="unsorted". In this document I don't find any hint on SetNmMdAndUqTags. With this document, but I don't know the function of this tool exactly. I don't know if I need to use SetNmMdAndUqTags before Markduplicates.