Hi David,
The original command I posted does filter the reads appropriately. I only
raised this as a collaborator was attempting to use samtools fastq and
complained of odd results (I've always used bamtofastq).
Looking at the documentation there is nothing indicating that collate is
required first which may be why people struggle with this.
IMO including a command line option to 'samtools fastq' to do the collation
would clarify this (default to no collation to preserve current behaviour, you
don't want the bedtools problem
<https://github.com/arq5x/bedtools2/issues/319>).
Regards,
Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute
k...@sanger.ac.uk
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104
> On 13 Feb 2017, at 10:59, David K. Jackson <david.jack...@sanger.ac.uk> wrote:
>
> On 08/02/2017 16:09, Keiran Raine wrote:
>
>> Looks like samtools fastq is broken:
> I think samtools fastq need a samtools collate first. You may also need to
> specify -F 0X900 .
> Does that help?
> David
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