[Samtools-help] sorting bam numerically vs lexicographically

[Ryan G. <gol...@um...>]

Hi - I've noticed that when sorting BAM files with samtools, the 
chromosomes are sorted lexicographically.  GATK insists on the 
chromosomes being sorted numerically.  I'm using Picard tools right now 
to make the conversion.

I thought, at first, the sorting was based on the order of the 
chromosomes in my fasta file when I indexed the genome, but that doesn't 
seem to matter.  Is there a way to have samtools sort the chromosomes 
numerically or match the order in the .fai file?  This could help 
eliminate a step that currently takes some time to run, perhaps as an 
option to the sort command?