Changes between Version 28 and Version 29 of SnpCallingPipeline

Timestamp:

Oct 16, 2010 6:18:52 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -36 +36 @@
                 "chr[1-24].fasta" -> align2
                 "chr[1-24].fasta" -> alignPE
-                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner (knownsOnly)"-> FixMateInformation" -> "flowcell_lane.aligned.bam"
+                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner (knownsOnly)"-> "FixMateInformation  (knownsOnly)" -> "flowcell_lane.aligned.bam"
                 "realign.intervals" -> "IndelRealigner (knownsOnly)"   
                 label = "Per Lane*Chromosome (750*3*24=54k) ";
@@ -45 +45 @@
                 color=lightgrey;
                 node [style=filled,color=white];
-                "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner"-> "FixMateInformation"
+                "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner"-> FixMateInformation
                 "flowcell_lane2.aligned.bam" -> Merge
                 "flowcell_lane3.aligned.bam" -> Merge
-                "FixMateInformation" -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
+                FixMateInformation -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
 Filtration -> VCF
                 label = "Per Sample*Chromosome (750*24=18k)";