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]

Back to Notebook

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.

  1. Read in the original .tsv files and save them as MATLAB structures
    1. Switch 5
  2. Read in the VCF data from the reference files, used for conversion to most hg19, and for writing the HAIR files
    1. Switch 6
  3. Reduce the memory (saves time)
    1. Switch 9
  4. Positional shift with the VCF data to convert the LFR to hg19
    1. Switches 7 and 8 at once
  5. Write the LFR data to a HAIR file
    1. Switch 10