Daniel:Notebook/Haplotyping/BACData

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Revision as of 20:56, 8 December 2015 by >Djacobse (→‎Processing)
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BAC Data Processing[edit]

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This page describes the data processing for the BAC data in the haplotyping project. For data locations, visit the Data Map.

Processing[edit]

  1. samtools targetcut
    1. Uses read depth from the data to assign reads into contigs
    2. Script
  2. Split the BAC Contigs by chromosome
    1. HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index
    2. Script
  3. Extract HAIRS
    1. HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome
    2. Script