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=LFR Data Processing= [[Daniel:Notebook/Haplotyping|Back to Notebook]] This page describes the data processing for the LFR data in the haplotyping project. For data locations, visit the [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1059932227 Data Map]. ==Data Processing== ===MATLAB=== The LFR data is principally processed using a [[File:Lfr_conversion_mcode.zip|matlab code]]. The [[Media:Lfr_conversion_master.txt|master file]] contains the architecture for converting the original LFR files to the output hair files. To perform the conversion, run the file lfr_conversion_master.m using the recommended switches. #Read in the original .tsv files and save them as MATLAB structures ##Switch 5 #Read in the VCF data from the reference files, used for conversion to most hg19, and for writing the HAIR files ##Switch 6 #Reduce the memory (saves time) ##Switch 9 #Positional shift with the VCF data to convert the LFR to hg19 ##Switches 7 and 8 at once #Write the LFR data to a HAIR file ##Switch 10
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