will using samtools merge to multiple bam files also remove the redundancy ?

Question

[naveedhasan2000]

So i have merged some bam files using the samtools merge -n command, i wanna know if the merged bam file which is made now will be non redundant or do i have to again use bedtools to remove the redundancy ?

[Pierre Lindenbaum]

how do you define " redundancy" ? if both bams are unrelated, the merged bam won't contain any common read.

[naveedhasan2000]

no the bams are not unrelated, they have common reads.

[bk11]

Are you talking about duplicate reads? If so, you can check the duplicates in your merged data simply by running-

samtools flagstat merged_data.bam

[GenoMax]

they have common reads.

As in they came from a single source sequence file and thus would have an identical fastq header?