Sorted vs unsorted SAM/BAM

Question

[ofonov]

Hi! I am quite new to NGS and could not find explanation of sorted and unsorted SAM/BAM files. How are these files sorted (what does SAMtool do to the file)? Why does it have to be done?

Thanks!

Answer 1

[mastal511]

Files can be sorted by coordinate (chromosomal position of the alignment), or by read name.

Some of the tools used for downstream analyses require sorted and indexed bam files.