Changes between Version 19 and Version 20 of ImputationPipeline


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Timestamp:
Nov 23, 2010 2:35:34 PM (12 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v19 v20  
    112112== IMPUTE2 pipeline ==
    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.
     114
     115{{#!graphviz
     116
     117digraph g {
     118a->b
     119}
     120
     121}}}
    114122=== ConvertBedBimFamToPedMap ===
    115123This script converts BED, BIM, FAM files to PED and MAP by using plink. The "Path to BED, BIM, FAM file" parameter should contain the path and the suffix of these files. For example if the files are: