When to use Sam Sort on a Bam file?

Question

[Arthur]

If a Bam file has been correctly collated using Sam Collate, should you also use Sam Sort when you have created a Sam file to sort the coordinates?

[Pierre Lindenbaum]

depends what you want to do with the sam. If a bam is sorted on coordinate, then it can be indexed with 'samtools index' and then you can quickly query a genomic region of the bam using random access instead of starting reading the whole bam from the beginning...