You could try the following for SAM -> BAM
samtools view -b -S file.sam > file.bam
Possibly this for BAM to SAM
samtools view -h -o out.sam in.bam
On Wed, Aug 27, 2014 at 11:36 PM, Radhouane Aniba <arad...@gmail.com> wrote:
> never mind I asked too fast
>
>
>
>
> On Wed, Aug 27, 2014 at 11:03 AM, Radhouane Aniba <arad...@gmail.com>
> wrote:
>
>> Hello guys
>>
>> Any examples of using samtools to convert from sam/bam to cram and vice
>> versa ?
>>
>> I cannot find in the doc how this is done via samtools (I see the help
>> and the -C option but not clear on how to use this)
>>
>> Thanks
>>
>> Rad
>>
>>
>
>
> --
> *Radhouane Aniba*
> *Bioinformatics Scientist*
> *BC Cancer Agency, Vancouver, Canada*
>
>
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