Changes between Version 49 and Version 50 of SnpCallingPipeline

Timestamp:

Oct 20, 2010 8:09:48 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -49 +49 @@
                 "chr[1-24].fasta" -> align2
                 "chr[1-24].fasta" -> alignPE
-                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" -> "flowcell_lane.aligned.bam"
+                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" ->"Quality Recalibration"->"flowcell_lane.aligned.bam"
                 "realign.intervals" -> "IndelRealigner & \n FixMateInformation (knownsOnly)"   
                 label = "Per Lane*Chromosome (750*3*24=54k) ";
@@ -57 +57 @@
                 style=filled;
                 color=lightgrey;
-                "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 -> "sample QC reports"
+                "IndelRealigner & FixMateInformation" -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "sample QC reports"
 Filtration -> "sample_chr[1-24].vcf"
-                label = "Per Sample*Chromosome (750*24=18k)";
+                label = "Per Sample or Trio*Chromosome (750*24=18k)";
         }
 }