Changes between Version 28 and Version 29 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 16, 2010 6:18:52 PM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v28 v29  
    3636                "chr[1-24].fasta" -> align2
    3737                "chr[1-24].fasta" -> alignPE
    38                 "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner (knownsOnly)"-> FixMateInformation" -> "flowcell_lane.aligned.bam"
     38                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner (knownsOnly)"-> "FixMateInformation  (knownsOnly)" -> "flowcell_lane.aligned.bam"
    3939                "realign.intervals" -> "IndelRealigner (knownsOnly)"   
    4040                label = "Per Lane*Chromosome (750*3*24=54k) ";
     
    4545                color=lightgrey;
    4646                node [style=filled,color=white];
    47                 "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner"-> "FixMateInformation"
     47                "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner"-> FixMateInformation
    4848                "flowcell_lane2.aligned.bam" -> Merge
    4949                "flowcell_lane3.aligned.bam" -> Merge
    50                 "FixMateInformation" -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
     50                FixMateInformation -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
    5151Filtration -> VCF
    5252                label = "Per Sample*Chromosome (750*24=18k)";