badly sorted BAM

[Filippo]

Hi,

I have some BAM files in which the chromosomes are sorted like characters, eg the first chromosome is 10, the second 11 and the last two are 8 and 9.

What is the quickest way to fix this? I tried samtools sort with no success.

Thanks!

[svl]

Hi Filippo, haven't tried this myself but perhaps you can use SortSam in Picard tools:

http://picard.sourceforge.net/command-line-overview.shtml#SortSam

Why do you want this specific order in an indexed file? Is it required by some tool?

[Filippo]

Hi, thanks for the answer, I will try it.
Do you think it would automatically sort the chromosomes or do I have to specify something?

I need them in a regular order (1,2,3 ... 22,X,Y) so that the following files (for example pileups made out of the bam) will also be in the regular order. The scripts that I made so far go crazy if they get chromosome 10 instead of 1.

[gringer]

I need them in a regular order (1,2,3 ... 22,X,Y) so that the following files (for example pileups made out of the bam) will also be in the regular order. The scripts that I made so far go crazy if they get chromosome 10 instead of 1.

Then you should probably change your scripts so that they can at least handle what samtools does. The people who write samtools also write the specification for SAM/BAM, so you need to be able to handle that format.

http://samtools.sourceforge.net/SAM1.pdf

This document says that the coordinate sort order in a SAM/BAM file must be based on the order of SQ lines in the header (p. 2, tag SO).