Changes between Version 13 and Version 14 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 14, 2010 11:57:41 PM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v13 v14  
    88
    99To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found in figure 1 & 2 in the appendix. The processes including commands, input and output files are described below, starting with pre-alignment.
    10 
    1110== Simplified Overview ==
    1211
     
    3332                "Lane1.aligned.bam" -> RealignIndelsAndFixMates2
    3433                "Lane2.aligned.bam" -> RealignIndelsAndFixMates2
    35                 "Lane2.aligned.bam" -> RealignIndelsAndFixMates2
     34                "Lane3.aligned.bam" -> RealignIndelsAndFixMates2
    3635                RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval
    3736Filtration -> VCF