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:



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  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 

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