Hi,
I suspect you will need to define the options before the input and region:
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region …]
i.e.
$ samtools view-U without-region.sam sample.bam 2:33050509-33154206
Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute
k...@sanger.ac.uk
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104
> On 8 May 2016, at 17:27, Peter Chovanec <peter.chova...@babraham.ac.uk> wrote:
>
> Hello,
>
> The question has been asked before here:
>
> https://www.biostars.org/p/183921/
>
> But the solution isn't very satisfactory. Why doesn't this work:
>
> samtools view sample.bam 2:33050509-33154206 -U without-region.sam
>
> or
>
> samtools view -b sample.bam 2:33050509-33154206 -o other_stuff.bam -U
> without-region.bam
>
> Thank you
>
> Peter
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