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Bio-Pipeline-Comparison-1.123050
River stage zero No dependents
++

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

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

Provides

Vcf3_2
in lib/Vcf.pm
Vcf3_3
in lib/Vcf.pm
Vcf4_0
in lib/Vcf.pm
Vcf4_1
in lib/Vcf.pm
VcfReader
in lib/Vcf.pm

Other files