Changes between Version 20 and Version 21 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 3:17:11 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v20 v21  
    113113impute2 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.
    114114
    115 {{#!graphviz
     115{{{#!graphviz
    116116
    117117digraph g {
    118 a->b
     118
     119        size="10,10"
     120
     121        node [shape=box,style=filled,color=white]
     122        "BED/BIM/FAM Files"
     123        "PED/MAP Files"
     124        "PED/MAP CHR1,CHR2,..."
     125        "GEN/Sample CHR1, CHR2,..."
     126        "GEN/Sample Imputed results"
     127
     128        "Recombination map"
     129        "Known haplotypes"
     130        "Information about the Reference SNPs"
     131
     132        node [shape=ellipse,color=yellow]
     133        ConvertBedBimFamToPedMap
     134        DividePedMapToChromosomes
     135        ConvertListsOfPedAndMapFilesToGenAndSample
     136        UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
     137        UseImpute2WithOnePhasedReferencePanel
     138
     139        subgraph cluster_0 {
     140
     141                style=filled;
     142                color=lightgrey;
     143
     144                "BED/BIM/FAM Files" -> ConvertBedBimFamToPedMap -> "PED/MAP Files"
     145                "PED/MAP Files" ->  DividePedMapToChromosomes ->  "PED/MAP CHR1,CHR2,..."
     146                "PED/MAP CHR1,CHR2,..." ->  ConvertListsOfPedAndMapFilesToGenAndSample ->  "GEN/Sample CHR1, CHR2,..."
     147
     148                label = "Convert Input Files to Gen / Sample format";
     149        }
     150
     151        subgraph cluster_1 {
     152
     153                style=filled;
     154                color=lightgrey;
     155
     156                "Recombination map"
     157                "Known haplotypes"
     158                "Information about the Reference SNPs"
     159
     160                label = "Reference data"
     161        }
     162
     163        subgraph cluster_2 {
     164
     165                style=filled;
     166                color=lightgrey;
     167
     168                "Recombination map" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
     169                "Known haplotypes" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
     170                "Information about the Reference SNPs" -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
     171                "GEN/Sample CHR1, CHR2,..." -> UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches
     172                UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches -> UseImpute2WithOnePhasedReferencePanel [label="For each batch"]
     173                UseImpute2WithOnePhasedReferencePanel -> "GEN/Sample Imputed results"
     174
     175                label = "Imputation";
     176        }
     177
    119178}
    120179