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

Copyright

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

2.3                                              September 2016                                         EAGLE(1)

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.

Name

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

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

   Inputoptionsforphasingwithoutareference:--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/outputoptionsforphasingusingareferencepanel:--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

   Regionselectionoptions:--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

   Algorithmoptions:--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)