Changes between Version 49 and Version 50 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 20, 2010 8:09:48 PM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v49 v50  
    4949                "chr[1-24].fasta" -> align2
    5050                "chr[1-24].fasta" -> alignPE
    51                 "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" -> "flowcell_lane.aligned.bam"
     51                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" ->"Quality Recalibration"->"flowcell_lane.aligned.bam"
    5252                "realign.intervals" -> "IndelRealigner & \n FixMateInformation (knownsOnly)"   
    5353                label = "Per Lane*Chromosome (750*3*24=54k) ";
     
    5757                style=filled;
    5858                color=lightgrey;
    59                 "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner"-> FixMateInformation
     59                "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner & FixMateInformation"
    6060                "flowcell_lane2.aligned.bam" -> Merge
    6161                "flowcell_lane3.aligned.bam" -> Merge
    62                 FixMateInformation -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "sample QC reports"
     62                "IndelRealigner & FixMateInformation" -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "sample QC reports"
    6363Filtration -> "sample_chr[1-24].vcf"
    64                 label = "Per Sample*Chromosome (750*24=18k)";
     64                label = "Per Sample or Trio*Chromosome (750*24=18k)";
    6565        }
    6666}