Re: [Samtools-help] sorting bam numerically vs lexicographically

[Alec W. <al...@br...>]

Hi Ryan,

Coordinate sort order is based on the order in which the @SQ lines 
appear in the header of the BAM file.  Coordinate sort order should be 
consistent between samtools, GATK and Picard, with the caveats that 
ordering of reads with the same coordinate is arbitrary, and ordering of 
unmapped reads that also do not have a coordinate is arbitrary.  I'm 
surprised that you say that GATK insists on a particular order.  I would 
think it would just require that they be in coordinate order as defined 
in the SAM spec.

-Alec

On 4/26/11 10:33 AM, Ryan Golhar wrote:
> 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?
>
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