Re: [Samtools-help] Sort and rmdup

[Daniel S. <so...@eb...>]

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,
>