Hi, On Mon, Sep 19, 2016 at 05:32:44PM +0800, peijia wrote: > I use samtools with the version 1.3.1 to execute the command "samtools > mpileup -uf REF.fasta merge.bam -o merge.bcf", the result shows "[mpileup] 1 > samples in 1 input files <mpileup> Set max per-file depth to 8000" and it > doesn't work.
Could we get more information please than "it doesn't work"? Do you get any more error messages? Is the exit code zero? (to see, run samtools-cmd; echo $?). Is the output file blank, or does it contain something? If so, is it a valid BCF file? I suspect you're outputting the textual mpileup and not BCF format (-g option). Try looking at the recommended workflows for example usage: http://www.htslib.org/workflow/ James -- James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- 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
