samtools failed to index if sorted by name

[TTYE]

Hi, I am relatively new to this field, please bear with me if my question is naive.

It works if -n is dropped. What should I do if I need the index file of sorted by name bam file for downstream analysis? The commands I used:

samtools sort -n aln.bam aln.sorted
samtools index aln.sorted.bam

[GenoMax]

See this thread for additional information: http://seqanswers.com/forums/showthread.php?t=16375

[TTYE]

Thanks GenoMax! This is very helpful! Appreciate!