Changes between Version 11 and Version 12 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 14, 2010 11:56:49 PM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v11 v12  
    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
     11== Simplified Overview ==
     12
     13This simplified overview hides intermediate sort and indexing steps.
     14
     15{{{#!graphviz
     16
     17digraph g {
     18  size="5,5"
     19
     20        subgraph cluster_0 {
     21                style=filled;
     22                color=lightgrey;
     23                node [style=filled,color=white];
     24                "Reads.1fq.gz" -> align1 -> alignPE
     25                "Reads.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "Lane.aligned.bam"
     26                label = "Per lane";
     27        }
     28
     29      subgraph cluster_1 {
     30                style=filled;
     31                color=lightgrey;
     32                node [style=filled,color=white];
     33                "Lane1.aligned.bam" -> RealignIndelsAndFixMates
     34                "Lane2.aligned.bam" -> RealignIndelsAndFixMates
     35                "Lane2.aligned.bam" -> RealignIndelsAndFixMates
     36                RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval
     37Filtration -> VCF
     38                label = "Per Sample";
     39        }
     40
     41
     42
     43
     44}
     45
     46
     47}}}
     48
     49
    1050
    1151== A. Pre-alignment ==