***samtools*** sort wrong???

[shuoguo]

Hi i used samtools to sort a bam file like this:
samtools sort my.bam my.out

i get a new bam file, but i wanted the new bam file to be sorted at the third column (FNAME) but not right

i check the result use

samtools view my.out.bam | awk '{print $3}' | uniq

what i got is something like:
chr1
chr10
chr11
...
chr2
chr20
...
chr3
chr4

I would like it to be:
chr1
chr2
chr3
...

thanks!!!

[swbarnes2]

That's a valid way of sorting, just not what you want.

I think Picard ReorderSam can reorder your .bam.

Or, change your chromosome names so they are Chr01 instead of Chr1. Then the numbers will alphabetize the way you want them to.

[shuoguo]

thank you!