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-...@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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