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Old 06-11-2010, 05:46 AM   #1
colindaven
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Location: Germany

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Default Samtools pileup coverage issue

Hi everyone,

I am trying to assess the alignment quality of two aligners.

It seems the samtools pileup command does not give data for every position in the genome.

Specifically, it does not print low coverage regions - coverage <3 from what I can see.

Is there a way to modify this behaviour ?

I see the -l FILE
at
http://samtools.sourceforge.net/samtools.shtml
may be helpful?

I want to include _all_ positions in the pileup.

Thanks
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Old 06-11-2010, 07:31 AM   #2
lh3
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No. You have to write a script to do this by yourself.
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Old 06-11-2010, 08:49 AM   #3
bbimber
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there's a good perl API for samtools if you want to go that route. google Bio:B::Samtools or something along those lines and you'll find it.
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