| This Release | Bio-Pipeline-Comparison-1.123050 | [Download] [Browse] | 31 Oct 2012 | |||
| Links | [ Discussion Forum ] [ View/Report Bugs ] [ Website ] [ Dependencies ] [ Other Tools ] | |||||
| 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 |
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| 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 |
| 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 |
