Re: [Samtools-help] sort order in Bam file

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

Hi Nirmala,

If the file was sorted by samtools and the problem is merely that the 
header has the wrong value, you can replace the header with samtools 
reheader or Picard ReplaceSamHeader.  If you do need to sort the file, 
check out the FAQ section about running out of memory: 
http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page#Q:___A_Picard_program_that_sorts_its_output_SAM.2FBAM_file_is_taking_a_very_long_time_and.2For_running_out_of_memory.__What_can_I_do.3F

-Alec

On 2/23/11 5:01 PM, Akula, Nirmala (NIH/NIMH) [C] wrote:
>
> ASSUME_SORTED=true command is not valid in GATK.
>
> I tried Picard sortsam.jar but got out of memory error. I am using
>
> >java --Xmx8g --jar picard/SortSam.jar I=sorted.bam 
> O=coordinateSorted.bam SORT_ORDER=coordinate
>
> Thanks,
>
> Nirmala
>
> ------------------------------------------------------------------------------------
>
> Nirmala Akula, MS, PhD
>
> Contractor,
>
> Human Genetics Branch
>
> NIMH/NIH
>
> Blg 35, Rm 1A/205
>
> Bethesda, MD - 20892
>
> Phone# 301-451-4258
>
> ------------------------------------------------------------------------
>
> *From:* Nils Homer [mailto:nil...@gm...]
> *Sent:* Wednesday, February 23, 2011 4:55 PM
> *To:* Akula, Nirmala (NIH/NIMH) [C]
> *Cc:* sam...@li...
> *Subject:* Re: [Samtools-help] sort order in Bam file
>
> If you have sorted the file you can use "ASSUME_SORTED=true" or use 
> "SortSAM.jar" to do the sorting.
>
> Nils
>
> On Wed, Feb 23, 2011 at 1:51 PM, Akula, Nirmala (NIH/NIMH) [C] 
> <ak...@ma... <mailto:ak...@ma...>> wrote:
>
> Hi,
>
>             I am using GATK to call SNPs in exome data and the program 
> gave an error message that BAM file is not co-ordinate sorted. I 
> looked at the header in the BAM file and it shows "SO:queryname".
>
>             I tried to use samtools reheader but that does not seem to 
> work. Here are commands:
>
> >Samtools view --H sorted.bam >myheader.txt
>
> >I edited myheader.txt by replacing "SO=queryname" to "SO=coordinate" 
> in EMACS
>
> >samtools reheader edited_myheader.txt sorted.BAM
>
> Thank you in advance for your responses.
>
> Regards,
>
> Nirmala
>
> ------------------------------------------------------------------------------------
>
> Nirmala Akula, MS, PhD
>
> Contractor,
>
> Human Genetics Branch
>
> NIMH/NIH
>
> Blg 35, Rm 1A/205
>
> Bethesda, MD - 20892
>
> Phone# 301-451-4258
>
>
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