Hello,
The Galaxy mpileup wrapper (available in the Tool Shed
http://usegalaxy.org/tool shed) or as implemented on the public Main
instance (http://usegalaxy.org), just uses the default, which is
8000 (option -D).
The SAMtools manual has the details, including the command-line for
the adjusting the max-file depth considered. The usage has a
specific use case, and is not used with SNP calling, but coverage
calculations:
http://samtools.sourceforge.net/mpileup.shtml
This is not to be confused with the per-sample position depth for
SNP calling (-d). This can be adjusted within the 1-8000 window. The
default is 250. If set to a value over 8000, the option -D will
override it before it can be applied, should the tool is given input
data that fits this criteria. Depending on the size of your input,
memory could still be an issue if depth is set very large. If there
is a memory related error, this is a probable cause, and a local or
cloud with sufficient resources is the alternative.
While max-file depth cannot be increased on the public server, in a
local instance the wrapper could be adjusted to include/specify the
-D parameter as an input option that can be modified.
This is the tool .xml (for ease of viewing, downloading the
repository is really best way to access the it in the most current
version):
http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=44a18a94d7a9&id=01d08a1b766b864e
Note from the manual usage in the SAMtools manual, that BAQ
calculations are not compatible with the choice to increase -D
(according to the tool authors), so adjust the tool form options at
execution time for this (the tool .xml will help with mapping
parameters, if the tool help in the UI is not enough). And finally,
be aware that this usage could significantly increase the memory
profile of the tool, so it is probably not appropriate for a local
on a personal desktop/laptop, but testing on your own data will
answer that definitively. A local run on a server or a cloud with
extended memory resources is most likely a better choice. In
general, if it runs on the line command, it will run in Galaxy, and
the reverse (fails line command, will fail in Galaxy - the
underlying tool is the same).
These were the constraints the last time the development team gave
feedback about the tool. If there are any updates, we will post
another reply. It is also possible that a member of our development
community has already modified the tool wrapper (but not submitted
it to the Tool Shed yet) and they will respond. I ran a search on
the getgalaxy archives (searches dev resources, and that includes
the galaxy-dev@bx.psu.edu mailing list), and didn't find anything
myself: http://galaxyproject.org/search/getgalaxy/
Hopefully this helps to explain and offer some choices.
Jen
Galaxy team
On 2/4/14 9:05 AM, Wang, Michael wrote:
Hi
All, one quick Q: how can I set max per-file depth to more
than 8000 under mpileup. Thanks!
Michael
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