Samtools pileup coverage issue

[colindaven]

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]

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

[bbimber]

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.