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Question: Want all counts on MPileup including zero counts
1
gravatar for ghalib.bardai
10 months ago by
ghalib.bardai • 10
ghalib.bardai • 10 wrote:

I am using the SAM tool MPileup application. The analysis parameters I use gives as an output the number of counts associated with coordinates. It does not however output coordinates with zero counts. I would like to have this information. Is there a way to do this?

Thanks

option tool mpileup samtools wrapper • 250 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by ghalib.bardai • 10
1
gravatar for y.hoogstrate
10 months ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

The arguments -a and -aa have not yet been implemented in the galaxy wrapper. This feature is BTW only available in the latest samtools version as samtools 1.3.1 does not even have it (but 1.6 does).
ADD COMMENT • link written 10 months ago by y.hoogstrate • 460
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