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EAGLE(1) General Commands Manual EAGLE(1)


eagle - Haplotype phasing within a genotyped cohort or using a phased reference panel


eagle [options]


Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. The basic idea of the Eagle1 algorithm is to harness identity-by-descent among distant relatives—which is pervasive at very large sample sizes but rare among smaller numbers of samples—to rapidly call phase using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.


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HapMap genetic map provided with download: tables/genetic_map_hg##.txt.gz
prefix for output files
number of computational threads

Input options for phasing without a reference:

prefix of PLINK .fam, .bim, .bed files
prefix of PLINK .fam.gz, .bim.gz, .bed.gz files
PLINK .fam file (note: file names ending in .gz are auto-decompressed)
PLINK .bim file
PLINK .bed file
[compressed] VCF/BCF file containing input genotypes
file(s) listing individuals to ignore (no header; FID IID must be first two columns)
file(s) listing SNPs to ignore (no header; SNP ID must be first column)
QC filter: max missing rate per SNP
QC filter: max missing rate per person

Input/output options for phasing using a reference panel:

tabix-indexed [compressed] VCF/BCF file for reference haplotypes
tabix-indexed [compressed] VCF/BCF file for target genotypes
b|u|z|v: compressed BCF (b), uncomp BCF (u), compressed VCF (z), uncomp VCF (v)
disable imputation of missing ./. target genotypes
allow swapping of REF/ALT in target vs. ref VCF

Region selection options:

chromosome to analyze (if input has many)
minimum base pair position to analyze
maximum base pair position to analyze
(ref-mode only) flanking region to use during phasing but discard in output

Algorithm options:

number of conditioning haplotypes
number of PBWT phasing iterations (0=auto)
expected length of haplotype copying (cM)
history length multiplier (0=auto)
estimated genotype error probability
in non-ref mode, use only PBWT iters (automatic for sequence data)
use Eagle1 phasing algorithm (instead of default Eagle2 algorithm)



Copyright © 2015-2016 Harvard University. Distributed under the GNU GPLv3+ open source license.

September 2016 2.3