Daniel:Notebook/Haplotyping/2014-7-8

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Mapped Phasing[edit]

This project can be split into two potential avenues. The first, and easiest, is to use the current reference genome and map everything to the reference. Then use the BAC pool data to identify variant calls within BACs and to begin phasing. The HiC data from Bing Ren's lab can be used to complete the phasing, and hopefully covers additional parts of the genome that the BACs cannot assess.

Mapping the bam files to hg19[edit]

The first step of the project will be to map the project to hg19, since the original BAC data was mapped to an older assembly. We'll do this using bwa, since it is fast and allows me to use .bam files as input.

Workflow[edit]

  1. Create index for bwa from hg19
    1. bwa index -p hg19 /home/kunzhang/HsGenome/hg19/hg19
  2. Run bwa on test file