---
name: "bio-eagle"
section: "1"
platform: "linux"
package: "bio-eagle"
version: "2.4.1-3+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bio-eagle"
---

# bio-eagle(1)

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

## 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

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