Samtools pileup coverage issue

colindaven · 06-11-2010, 05:46 AM

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

lh3 · 06-11-2010, 07:31 AM

No. You have to write a script to do this by yourself.

bbimber · 06-11-2010, 08:49 AM

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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06-11-2010, 05:46 AM	#1
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	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

06-11-2010, 08:49 AM	#3
bbimber Member Location: wisconsin Join Date: Jan 2010 Posts: 12	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.

06-11-2010, 07:31 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	No. You have to write a script to do this by yourself.