Daniel:Notebook/Haplotyping/BEAGLE: Difference between revisions

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=Processing LFR and Hi-C Data=
=Processing BEAGLE Data=


[[Daniel:Notebook/Haplotyping|Back to Notebook]]
[[Daniel:Notebook/Haplotyping|Back to Notebook]]


This page describes the data processing for the LFR-BAC-HiC combined data in the haplotyping project. For data locations, visit the [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=676014356 Data Map].
This page describes the data processing for the BEAGLE data in the haplotyping project. For data locations, visit the [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=676014356 Data Map].


*The BEAGLE manual can be found [http://faculty.washington.edu/browning/beagle/beagle_4.1_21Oct15.pdf here]
*The BEAGLE manual can be found [http://faculty.washington.edu/browning/beagle/beagle_4.1_21Oct15.pdf here]


==Processing==
==Processing==
#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).
##[[Media:Overlap_checker.sh|Shell file]] for looping through protocol and [[Media:Overlap_checker.txt|MATLAB file]]
#Next, we run BEAGLE
##[[Media:Impute_vcf_BEAGLE.sh|Shell script]] for BEAGLE imputations

Latest revision as of 21:50, 9 December 2015

Processing BEAGLE Data[edit]

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[edit]

  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
  2. Next, we run BEAGLE
    1. Shell script for BEAGLE imputations