Hi Joao,
Recent versions of samtools write to stdout and let you choose the output
format
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
-@ INT Set number of sorting and compression threads [1]
Colin
On 20 August 2015 at 18:12, Joao Dias <[email protected]> wrote:
> Good morning,
> I am wondering if you received my previous email.
> Thank you in advance.
>
> Regards,
> João Dias
>
> From: Joao Dias <[email protected]>
> Date: Wednesday, 12 August 2015 09:34
> To: "[email protected]" <
> [email protected]>
> Subject: samtools sort
>
> Good morning,
> I am wondering if it is possible to sort a bam file as a standard output
> without saving for a samtools mpileup command.
> Thank you,
> Joao
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
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