Daniel:Notebook/Haplotyping/BACData
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BAC Data Processing
This page describes the data processing for the BAC data in the haplotyping project. For data locations, visit the Data Map.
Processing
- samtools targetcut
- Uses read depth from the data to assign reads into contigs
- Script
- Split the BAC Contigs by chromosome
- HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index
- Script
- Extract HAIRS
- HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome
- script