The following module was proposed for inclusion in the Module List:
modid: Annovar::Wrapper
DSLIP: adpOp
description: Wrapper around the annotation tool annovar.
userid: JILLROWE (Jillian Rowe)
chapterid: 8 (User_Interfaces)
communities:
https://github.com/jerowe/wrapper-annovar
similar:
Bio::Tools::WrapperMaker
rationale:
This is a tool specifically to automate a pipeline to go from VCF
files -> annovar annotation files -> annotated VCF files.
Reannotating the VCF file is optional.
To this end it takes as its input a vcf file, or a list of vcf
files, gets the sampleIDs contained within, and writes the annovar
input conversion, annovar annotation commands, and the commands to
write out a new annotated vcf. It also places files in a tree
structure with annovar_interim, annovar_final, vcf-annotate_interim,
and vcf-annotate_final. That way a user can clearly distinguish
between the generated interim files and the final output file.
I could have written something similar using
Bio::Tools::WrapperMaker, but I prefer wrappers written in Moose
with MooseX::Getopt, and I wanted to protect against very large
STDOUT/STDERR by IPC::Open3 and IO::Select.
In conjunction with Runner::Threads/MCE many of the processes can
be run in parallel, with a 'wait' command for any jobs that need to
complete before the next one can begin.
enteredby: JILLROWE (Jillian Rowe)
enteredon: Tue Jun 24 10:48:49 2014 UTC
The resulting entry would be:
Annovar::
::Wrapper adpOp Wrapper around the annotation tool annovar. JILLROWE
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