Hi Lev,
They'll be in whatever order your shell expands *.bam to, as it's the shell
that takes care of this. This will normally be alphabetic, but you can
often configure your shell to use a different order (google "glob file
order shell" for more than you ever wanted to know about this). You can
also change the language localization, which can then change what order the
alphabet is in (keep this in mind if you share scripts with colleagues).
Best,
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<[email protected]>
On Sun, Aug 31, 2014 at 9:26 PM, Yampolsky, Lev <[email protected]>
wrote:
> Let’s say I generate an mplileup file feeding .BAM files to samtools as
> *.BAM. Should I assume the samples are ordered in the mpileup
> alphabetically, by .BAM filename?
>
> What if I list BAMs as "zzz.BAM, aaa.BAM"? Still alphabetically or in the
> order listed in the command line?
>
> Thanks!
>
>
> --
> Lev Yampolsky
>
> Professor
> Department of Biological Sciences
> East Tennessee State University
> Box 70703
> Johnson City TN 37614-1710
> Cell 423-676-7489
> Office/lab 423-439-4359
> Fax 423-439-5958
>
>
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