Sorted vs unsorted SAM/BAM

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!

sort sam bam samtools

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updated 10.4 years ago by mastal511

• written 10.4 years ago by ofonov •

1 answer

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.

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written 10.4 years ago by mastal511

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