Hi,

I would like to know whether one needs to sort and to index the .bam files again after removing the duplicates in Samtools using `samtools rmdup -S`.

I am under the impression that since we have already sorted and indexed the .bam files, and we are just removing the duplicates, there would be no need to do the sorting and indexing again. Am I wrong?

Thanks in advance for your thoughts!
"sort"

no: your bam is already sorted.

"index"

yes if you need to access some specific genomic regions in your bam. The previous index of the bam cannot be used with the new rmdup.bam