Hi Keiran,
Still only produced an empty BAM.
Kind regards,
Peter
On 09/05/16 09:12, Keiran Raine wrote:
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
<mailto:[email protected]>[email protected]<mailto:[email protected]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104
On 8 May 2016, at 17:27, Peter Chovanec
<<mailto:[email protected]>[email protected]<mailto:[email protected]>>
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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