Daniel:Notebook/Haplotyping/LFRData: Difference between revisions
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===MATLAB=== | ===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. | 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 | #Read in the original .tsv files and save them as MATLAB structures |
Latest revision as of 21:19, 8 December 2015
LFR Data Processing[edit]
This page describes the data processing for the LFR data in the haplotyping project. For data locations, visit the Data Map.
Data Processing[edit]
MATLAB[edit]
The LFR data is principally processed using a matlab code. The 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