Hi Joao, The short answer is no.
For most uses of for coordinate sorted BAM files (e.g. mpileup) random access is performed (via the assosicated BAM index), and therefore having the input BAM file on stdin is not possible. However, you can output samtools sort to stdout (see the -o option). For name sorted BAM output, this is probably quite useful. Peter On Wed, Aug 12, 2015 at 9:41 AM, Joao Dias <j...@sanger.ac.uk> wrote: > 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 > Euston Road, London, NW1 2BE. > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
