sorted by name or coordinate sorted

[papori]

Hi all,
I am working on bam files from the TCGA.
In the header of the bam, there is:
SORTED
As i understood, it is sorted by coordinates.
In samtools there is option -n, which is sorted by name.

Is it the same?

As far i understand - coordinates is the seq-machine coordinates, and name is the name of the read - so it seems the same to me..

Any comments?

Thanks,
Pap

[maubp]

No, they are not the same.

Name sorting looks at the read names (which can be derived from positions on the sensor).

Coordinate sorting refers to sorting based on the mapping positions (and can only be used if you have mapper your reads onto a reference genome/assembly). This is the default sorting and is essential for BAM viewers and used for things like SNP analysis.