bio-eagle(1)

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

Section 1 bio-eagle bookworm source

Description

EAGLE

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 relativesâwhich is pervasive at very large sample sizes but rare among smaller numbers of samplesâto 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)