Bioperl and Samtools

Question

How can I run 'mpileup' using Bioperl ?

When trying to run mpileup using Bio::Tools::Run::Samtools , I am getting 'mpileup' is not registered. What am I doing wrong? Any pointers towards the right direction are appreciated... thank you guys.....

Answer 1

The short answer is you cannot run mpileup using BioPerl-Run because, as your error message describes, that command does not appear to be listed as one available to samtools. You might want to raise this issue on the bioperl-listserv, and hopefully someone will add this feature.