Changes between Version 20 and Version 21 of ImputationPipeline

Timestamp:

Nov 23, 2010 3:17:11 PM (15 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -113 +113 @@
 impute2 accepts only gen and sample files as input files. So we may have to perform some format conversions before running impute2. If our initial datasets are Ped and Map files then we can use the method: ConvertManyPedMapToGenSample to convert it to gen and sample files. If our initial datasets are in Bed/Bim/Fam format then we can use ConvertBedBimFamToPedMap to convert to Ped and Map files and then use ConvertManyPedMapToGenSample to convert to gen and sample files. As soon as you are done with these conversions steps you can use the UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches to perform the imputation. This method has to be run once for each chromosome. 
 
-{{#!graphviz
+{{{#!graphviz
 
 digraph g {
-a->b
+
+        size="10,10"
+
+        node [shape=box,style=filled,color=white]
+        "BED/BIM/FAM Files"
+        "PED/MAP Files"
+        "PED/MAP CHR1,CHR2,..."
+        "GEN/Sample CHR1, CHR2,..."
+        "GEN/Sample Imputed results"
+
+        "Recombination map"
+        "Known haplotypes"
+        "Information about the Reference SNPs"
+
+        node [shape=ellipse,color=yellow]
+        ConvertBedBimFamToPedMap
+        DividePedMapToChromosomes
+        ConvertListsOfPedAndMapFilesToGenAndSample
+        UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
+        UseImpute2WithOnePhasedReferencePanel
+
+        subgraph cluster_0 {
+
+                style=filled;
+                color=lightgrey;
+
+                "BED/BIM/FAM Files" -> ConvertBedBimFamToPedMap -> "PED/MAP Files"
+                "PED/MAP Files" ->  DividePedMapToChromosomes ->  "PED/MAP CHR1,CHR2,..."
+                "PED/MAP CHR1,CHR2,..." ->  ConvertListsOfPedAndMapFilesToGenAndSample ->  "GEN/Sample CHR1, CHR2,..."
+
+                label = "Convert Input Files to Gen / Sample format";
+        }
+
+        subgraph cluster_1 {
+
+                style=filled;
+                color=lightgrey;
+
+                "Recombination map"
+                "Known haplotypes"
+                "Information about the Reference SNPs"
+
+                label = "Reference data"
+        }
+
+        subgraph cluster_2 {
+
+                style=filled;
+                color=lightgrey;
+
+                "Recombination map" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
+                "Known haplotypes" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
+                "Information about the Reference SNPs" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
+                "GEN/Sample CHR1, CHR2,..." -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
+                UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches -> UseImpute2WithOnePhasedReferencePanel [label="For each batch"]
+                UseImpute2WithOnePhasedReferencePanel -> "GEN/Sample Imputed results"
+
+                label = "Imputation";
+        }
+
 }