Filter Pileup in SAM tools

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Filter Pileup in SAM tools

Andrew South

NGS: SAM Tools

 

I have generated a simple 6 column pileup from my BAM file but when I try to use the Filter Pileup tool it doesn’t recognise my pileup file, I receive the message “History does not include a dataset of the required format / build”. Build is hg19. Curiously in the same history I have ran the tool through a workflow without a hitch.

 

Any advice to successfully filter my pileup would be gratefully received.

 

Many thanks,


Andy


The University of Dundee is a registered Scottish Charity, No: SC015096
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Re: Filter Pileup in SAM tools

Anton Nekrutenko
<base href="x-msg://582/">Andy:

This is an issue we are aware of. To workaround is:

- click on a pencil icon within the pileup dat set you nee to filter
- middle pane on the interface will change
- click on "datatype" tab
- select "pileup" in "New datatype"
- click save

Filter pileup will now recognize you dataset.

Thanks and sorry for late reply.

anton


On Feb 22, 2013, at 3:58 AM, Andrew South wrote:

NGS: SAM Tools

 

I have generated a simple 6 column pileup from my BAM file but when I try to use the Filter Pileup tool it doesn’t recognise my pileup file, I receive the message “History does not include a dataset of the required format / build”. Build is hg19. Curiously in the same history I have ran the tool through a workflow without a hitch.

 

Any advice to successfully filter my pileup would be gratefully received.

 

Many thanks,

Andy

The University of Dundee is a registered Scottish Charity, No: SC015096 ___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/