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

EAGLE(1) General Commands Manual EAGLE(1)

NAME

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

SYNOPSIS

eagle [ options]

DESCRIPTION

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.

OPTIONS

-h, --help
Print this help
--geneticMapFile arg
HapMap genetic map provided with download: tables/genetic_map_hg##.txt.gz
--outPrefix arg
prefix for output files
--numThreads arg (=1)
number of computational threads

Input options for phasing without a reference:

--bfile arg
prefix of PLINK .fam, .bim, .bed files
--bfilegz arg
prefix of PLINK .fam.gz, .bim.gz, .bed.gz files
--fam arg
PLINK .fam file (note: file names ending in .gz are auto-decompressed)
--bim arg
PLINK .bim file
--bed arg
PLINK .bed file
--vcf arg
[compressed] VCF/BCF file containing input genotypes
--remove arg
file(s) listing individuals to ignore (no header; FID IID must be first two columns)
--exclude arg
file(s) listing SNPs to ignore (no header; SNP ID must be first column)
--maxMissingPerSnp arg (=0.1)
QC filter: max missing rate per SNP
--maxMissingPerIndiv arg (=0.1)
QC filter: max missing rate per person

Input/output options for phasing using a reference panel:

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

Region selection options:

--chrom arg (=0)
chromosome to analyze (if input has many)
--bpStart arg (=0)
minimum base pair position to analyze
--bpEnd arg (=1e9)
maximum base pair position to analyze
--bpFlanking arg (=0)
(ref-mode only) flanking region to use during phasing but discard in output

Algorithm options:

--Kpbwt arg (=10000)
number of conditioning haplotypes
--pbwtIters arg (=0)
number of PBWT phasing iterations (0=auto)
--expectIBDcM arg (=2.0)
expected length of haplotype copying (cM)
--histFactor arg (=0)
history length multiplier (0=auto)
--genoErrProb arg (=0.003)
estimated genotype error probability
--pbwtOnly
in non-ref mode, use only PBWT iters (automatic for sequence data)
--v1
use Eagle1 phasing algorithm (instead of default Eagle2 algorithm)

SEE ALSO

https://data.broadinstitute.org/alkesgroup/Eagle/ Copyright © 2015-2016 Harvard University. Distributed under the GNU GPLv3+ open source license.
September 2016 2.3