Changes between Version 11 and Version 12 of SnpCallingPipeline

Timestamp:

Oct 14, 2010 11:56:49 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -8 +8 @@
 
 To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found in figure 1 & 2 in the appendix. The processes including commands, input and output files are described below, starting with pre-alignment.
+
+== Simplified Overview ==
+
+This simplified overview hides intermediate sort and indexing steps.
+
+{{{#!graphviz
+
+digraph g {
+  size="5,5"
+
+        subgraph cluster_0 {
+                style=filled;
+                color=lightgrey;
+                node [style=filled,color=white];
+                "Reads.1fq.gz" -> align1 -> alignPE
+                "Reads.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "Lane.aligned.bam"
+                label = "Per lane";
+        }
+
+      subgraph cluster_1 {
+                style=filled;
+                color=lightgrey;
+                node [style=filled,color=white];
+                "Lane1.aligned.bam" -> RealignIndelsAndFixMates 
+                "Lane2.aligned.bam" -> RealignIndelsAndFixMates
+                "Lane2.aligned.bam" -> RealignIndelsAndFixMates
+                RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval
+Filtration -> VCF
+                label = "Per Sample";
+        }
+
+
+
+
+}
+
+
+}}}
+
+
 
 == A. Pre-alignment ==