Documentation

BeagleCodec

Codec for Beagle imputation engine

Category ROD Codecs


Overview

Reads in tabular files with site markers and genotype posteriors, genotypes and phasing that Beagle produced

See also: @see BEAGLE home page

File format example for phased genotypes file

     dummy header
      20:60251 T T T T T T
      20:60321 G G G G G G
      20:60467 G G G G G G
 

File format example for genotype posteriors

     marker alleleA alleleB NA07056 NA07056 NA07056
     20:60251 T C 0.9962 0.0038 0 0.99245 0.00755 0 0.99245 0.00755 0
     20:60321 G T 0.98747 0.01253 0 0.99922 0.00078 0 0.99368 0.00632 0
     20:60467 G C 0.97475 0.02525 0 0.98718 0.01282 0 0.98718 0.01282 0
 

File format example for r2 file
      20:60251        0.747
      20:60321        0.763
      20:60467        0.524
 


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA