Daniel:Notebook/Haplotyping/LFRData: Difference between revisions

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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.
#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

Revision as of 21:18, 8 December 2015

LFR Data Processing

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

MATLAB

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.

  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