Changes between Version 18 and Version 19 of ImputationPipeline
- Timestamp:
- Nov 23, 2010 2:32:02 PM (14 years ago)
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ImputationPipeline
v18 v19 110 110 That's basically it. A lot simpler than the previous version, don't you think? The required tool is attached to this e-mail, but might still be a bit buggish. Any recommendations are therefore more than welcome. 111 111 112 == IMPUTE pipeline == 112 == IMPUTE2 pipeline == 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. 113 114 === ConvertBedBimFamToPedMap === 114 115 This 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:
