Daniel:Notebook/Haplotyping/BEAGLE

From ZhangLabWiki
Revision as of 21:48, 9 December 2015 by >Djacobse (→‎Processing LFR and Hi-C Data)
Jump to navigation Jump to search

Processing BEAGLE Data

Back to Notebook

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

  • The BEAGLE manual can be found here

Processing

  1. BEAGLE requires a starting genotyping file. This file needs to include all genotypes at all the relevant sites. Sites that are known can have a 0|1 or 1|0. Sites that are unknown are a 0/1. For the purposes of this project, I first started with the Hi-C data, but it can be done with any hapcut output file. The first step in the pipeline converts a HAPCUT output file to a vcf with the genotypes assigned for the largest block (given 0|1 or 1|0). The other SNPs are imputed by BEAGLE (assigned 0/1 by the program).
    1. shell file for looping through protocol and MATLAB file