Changes between Version 20 and Version 21 of SnpCallingPipeline

Timestamp:

Oct 16, 2010 5:59:25 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -32 +32 @@
                 color=lightgrey;
                 node [style=filled,color=white];
-                "Reads.1fq.gz" -> align1 -> alignPE
+                "flowcell_lane.1fq.gz" -> align1 -> alignPE
                 "chr[1-24].fasta" -> align1
                 "chr[1-24].fasta" -> align2
                 "chr[1-24].fasta" -> alignPE
-                "Reads.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "Lane.aligned.bam"
+                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "flowcell_lane.aligned.bam"
                 "realign.intervals" -> RealignIndelsAndFixMates   
                 label = "Per lane/Per chromosome";
@@ -45 +45 @@
                 color=lightgrey;
                 node [style=filled,color=white];
-                "Lane1.aligned.bam" -> RealignIndelsAndFixMates2 
-                "Lane2.aligned.bam" -> RealignIndelsAndFixMates2
-                "Lane3.aligned.bam" -> RealignIndelsAndFixMates2
+                "flowcell_lane.aligned.bam" -> RealignIndelsAndFixMates2 
+                "flowcell_lane2.aligned.bam" -> RealignIndelsAndFixMates2
+                "flowcell_lane3.aligned.bam" -> RealignIndelsAndFixMates2
                 RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
 Filtration -> VCF