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Family members. Controls. SNP data. SNP data. Windows. direct import. selection of markers eliminate typing errors eliminate markers with MAF=0 or no call. allele frequency. Pedin. pre. parameters for Allegro, Merlin. Reference LD data file. Hapmap data.

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  1. Family members Controls SNP data SNP data Windows direct import • selection of markers • eliminate typing errors • eliminate markers with MAF=0 or no call allele frequency Pedin.pre • parameters for Allegro, Merlin Reference LD data file Hapmap data • inter-marker distances • LD setting (D’, r2) Annotation file Batch_filename.lkin Annotation file (affymetrix) Batch_filename.lkin run_linkage.pl generate datafile.dat, pedin.pre and option file output.zip Directories of each chromosome Outputfile, haplotype prediction run Allegro, Merlin for defined markers Unix

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