| 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¶
COPYRIGHT¶
Copyright © 2015-2016 Harvard University. Distributed under the GNU GPLv3+ open source license.
| September 2016 | 2.3 |