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

[Sean D. <sd...@ma...>]

On Tue, Apr 26, 2011 at 10:52 AM, Alec Wysoker <al...@br...> wrote:
> 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.

I think you can run GATK with the "unsafe" option and it will take
files not in "karyotype order".  However, I have been encouraging
folks I interact with to carefully sort the reference genome fasta
files in karyotype order so that everything downstream follows nicely
in karyotype order.

I agree with Alec that insisting on a specific order seems odd for
GATK to adopt, but they must have their reasons.

Sean


> 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?
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> Samtools-help mailing list
>> Sam...@li...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>