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Old 04-01-2013, 12:07 PM   #1
asebastian
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Location: USA

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Default BioPerl & Variant calling

Hi ,

I am trying to do variant calling with mpileup using BioPerl.
I am using Bio::Tools::Run::Samtools but it says mpileup not registered.
Does this mean BioPerl doesn't support mpileup ?
Can anyone tell me how to run it(or any other variant calling program) through a BioPerl module ?

Thank you
-As
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Old 04-02-2013, 02:37 AM   #2
davidblaney
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Default

Hi,

After looking at CPAN and then at the module code directly it looks as if mpileup is not supported as there is no '-command' option in the code.

This may be because the module was written for an old version of samtools and so mpileup was not implemented.

you could email them [BioPerl] and see if they will write in support as I am guessing it would be useful for other people and relatively simple to do. Otherwise have you considered using system calls in perl to run mpileup?

Code:
system("samtools mpileup ......");
D
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Old 04-02-2013, 12:57 PM   #3
asebastian
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Thanks David,
With BioPerl, I am trying to contact them...
As for the system calls, I am trying to avoid direct system commands... Thats why I was looking for a BioPerl wrapper...

-A
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