merging bam files with samtools

[tahamasoodi]

Hi,

I'm using merge option in samtools for merging bam files. Just one query, do I need to first sort each bam file before merging or I've to sort the merged bam file?

[FractalExpression]

My understanding is that you should perform all upstream processing (e.g. merging, fixing headers, etc) and then sort. As the output from some functions are unsorted.

[tahamasoodi]

Is there any more input?

[tahamasoodi]

I think, any option can be taken as the results are same.