Re: [Samtools-help] Sort and rmdup

[Tom B. <tb...@um...>]

For a quick fix, you might try using the '-m' flag to give 
samtools sort enough memory to avoid any need for temp files. 
E.g.  'samtools sort -m 8000000000 -o - temp.sorted | ...' 
for 8 Gb RAM, assuming you have that much physical memory.

 	 	 	 	 	-  tom blackwell  -

On Fri, 16 Apr 2010, Daniel Sobral wrote:

> I'm having similar problems.
> What seems to be happening in my case is that there are for some reason
> problems with the temp files that get created during sorting.
>
> Daniel
>
> On 16/04/2010 07:03, Henrikki Almusa wrote:
>> Hi,
>>
>> I've tried to use the piping from sort but it seems to fail. If I run
>> the two commands:
>>
>> samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
>>    samtools sort - raw-sorted
>> samtools rmdup raw-sorted.bam sorted.bam
>>
>> This produces a 1.8Gb sorted bam file. However if I try to use the
>> piping the sort:
>>
>> samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
>>    samtools sort -o - raw-sorted | samtools rmdup - sorted.bam
>>
>> I get 163 Mb bam file. What causes the difference?
>>
>> Thanks,
>>
>
>
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