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  • 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

  • #2
    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

    Comment


    • #3
      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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