Andrew Page > Bio-Pipeline-Comparison-1.123050

Bio-Pipeline-Comparison-1.123050

This Release Bio-Pipeline-Comparison-1.123050  [Download] [Browse 31 Oct 2012
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Repository https://github.com/sanger-pathogens/Bio-Pipeline-Comparison.git
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License The GNU General Public License, Version not specified
Special Files
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::Pipeline::Comparison Comparative assesment of variant calling (CAVar)      
Bio::Pipeline::Comparison::Exceptions Custom exceptions      
Bio::Pipeline::Comparison::Generate::Evolve Take in a reference genome and evolve it.      
Bio::Pipeline::Comparison::Generate::EvolvedSet Take in a reference genome and evolve it multiple times to produce multiple FASTA files and VCF files containing the differences to the original reference.      
Bio::Pipeline::Comparison::Generate::VCFWriter Create a VCF with the differences between a reference and a single evolved genome. Outputs a gzipped VCF file and a tabix file.      
Bio::Pipeline::Comparison::Report::InputParameters Take in a set of input parameters for the evalute pipeline functionality, validate them, then manipulate them into a usable set.      
Bio::Pipeline::Comparison::Report::Overview Aggregate together the results of multiple VCF comparisons      
Bio::Pipeline::Comparison::Report::ParseVCFCompare Take in the output of VCF compare and return details about intersection of variants.      
Bio::Pipeline::Comparison::Types Moose types to use for validation      
Bio::Pipeline::Comparison::Validate::Executable Validates the executable is available in the path before running it      
FaSlice FaSlice.pm from VCFTools      
Vcf Vcf.pm from VCFTools     r779

Documentation

evaluate_pipeline Take in a VCFs of known variants and observed variants and output a report  
evolve_genome Take in a reference genome and evolve it.  
vcf-compare VCF comparison script from VCFTools