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)

COPYRIGHT

September 2016

2.3