Ubuntu Manpage: Beagle - Genotype calling, genotype phasing and imputation of ungenotyped markers

Provided by: beagle_220722-1_all

NAME

       Beagle - Genotype calling, genotype phasing and imputation of ungenotyped markers

SYNOPSIS

       java -Xmx[GB]g -jar /usr/share/beagle/beagle.jar [options]

DESCRIPTION

       Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and
       identity-by-descent segment detection. Genotypic imputation  works  on  phased  haplotypes
       using a Li and Stephens haplotype frequency model.  Beagle also implements the Refined IBD
       algorithm  for  detecting  homozygosity-by-descent  (HBD)  and  identity-by-descent  (IBD)
       segments.

OPTIONS

Data input/output parameters
gt=filename
Optional
Specifies a VCF file containing a GT (genotype) format field for each marker. If a
genotype contains the phased allele separator, "|", then Beagle will preserve the
phase of the genotype during the analysis. If you use the gt argument, all
genotypes in the output file will be phased and non-missing.

gl=filename
Optional
Specifies a VCF file containing a GL or PL (genotype likelihood) format field for
each marker. Any data in the GT format field will be ignored. If both GL and PL
format fields are present for a marker, the GL format will be used.

gtgl=filename
Optional
Specifies a VCF file containing a GT, GL or PL format field for each marker. If a
genotype is non-missing, Beagle will ignore the genotype likelihood. If both GL
and PL format fields are present for a marker, the GL field will be used.

ref=filename
Optional
Specifies a VCF file containing phased reference genotypes. See the impute
parameter.

out=prefix
Required
Specifies the output filename prefix. The prefix may be an absolute or relative
filename, but it cannot be a directory name.

excludesamples=filename
Optional
Specifies a file containing non-reference samples (one sample per line) to be
excluded from the analysis and output files.

excludemarkers=filename
Optional
Specifies a file containing markers (one marker per line) to be excluded from the
analysis and the output files. An excluded marker identifier can either be an
identifier from the VCF record’s ID field or a genomic coordinate in the format:
CHROM:POS.

map=filename
Optional
Specifies a PLINK format genetic map on the cM scale. HapMap GrCh36 and GrCh37
genetic maps in PLINK format are available for download from the Beagle website.
Use of a genetic map is recommended if you are imputing ungenotyped markers. If no
genetic map is specified, Beagle will assume a constant recombination rate of 1 cM
/ Mb.

chrom=chrom:start-end
Optional
Specifies a chromosome or chromosome interval using a chromosome identifier in the
VCF file and the starting and ending positions of the interval. The entire
chromosome, the beginning of the chromosome, and the end of a chromosome can be
specified by chrom=[chrom], chrom=[chrom:-end], and chrom=[chrom:start-]
respectively.

maxlr=number_≥_1
Default = 5000
Specifies the maximum likelihood ratio at a genotype. If M is the maximum of the
likelihoods of each possible genotype, any likelihood that is less than (M ⁄ maxlr)
is set to 0.0 to improve computational efficiency.

General parameters
nthreads=positive_integer
Default: machine-dependent
Specifies the number of threads of execution. If no nthreads parameter is
specified, the nthreads parameter will be set equal to the number of CPU cores on
the host machine.

lowmem=true/false
Default = false
Specifies whether a memory efficient algorithm should be used. The memory
efficient algorithm increases run-time by a factor less than 2.0.

window=positive_integer
Default = 50000
Specifies the number of markers to include in each sliding window. The window
parameter must be at least twice as large as the overlap parameter. The window
parameter controls the amount of memory used in the analysis. For human data, it
is recommended that the window parameter be greater than or equal to the typical
number of markers in 5 cM.

overlap=positive_integer
Default = 3000
Specifies the number of markers of overlap between sliding windows. For human
data, it is recommended that the overlap be set to the typical number of markers in
0.5 cM (when ibd=false) or 2.0 cM (when ibd=true).

seed=integer
Default = -99999
Specifies the seed for the random number generator.

Phasing and imputation parameters
niterations=non-negative_integer
Default = 5
Specifies the number of phasing iterations. The phasing iterations are preceded by
10 burn-in iterations which carry out the Beagle version 4.0 phasing algorithm. If
you want to phase your data with the Beagle 4.0 phasing algorithm, use
niterations=0. Accuracy and compute time increase with the number of iterations.

impute=true/false
Default = true
Specifies whether markers that are present in the reference panel but absent in
your data will be imputed. This option has no effect if the ref and gt arguments
are not used.

gprobs=true/false
Default = false
Specifies whether a GP (genotype probability) format field will be included in the
output VCF file when imputing ungenotyped markers. By default, a GP fields is not
printed because a DS (alternate allele dose) format field is always printed when
imputing ungenotyped markers.

ne=integer
Default = 1000000
Specifies the effective population size when imputing ungenotyped markers. The
default value is suitable for a large outbred human population. Smaller values in
the hundreds or thousands for the ne parameter are suggested for inbred human and
animal populations.

err=non-negative_number
Default = 0.0001
Specifies the allele miscall rate. The default value should give good results for
most sequence and SNP array data.

cluster=non-negative_number
Default = 0.005
Specifies the maximum cM distance between individual markers that are combined into
an aggregate marker when imputing ungenotyped markers.

IBD parameters
ibd=true/false
Default = false
Specifies whether IBD analysis will be performed when the gt argument is used.

ibdlod=non-negative_integer
Default = 3.0
Specifies the minimum LOD score for reported IBD.

ibdscale=non-negative_number
Default: data-dependent
Specifies the scale parameter used to build the haplotype frequency model for IBD
analysis. If no ibdscale parameter is specified the scale parameter for the IBD
analysis will be set to max{2, sqrt[sample size]/100}, which we have found to work
well for outbred populations.

ibdtrim=non-negative_integer
Default = 40
Specifies the number of markers trimmed from the end of a shared haplotype when
testing for IBD. Note: The default ibdtrim parameter is designed for European
samples genotyped with a 1M SNP array (~ 1 marker per 3 kb). For human SNP array
data, it is recommended to set the ibdtrim parameter to the typical number of
markers in a 0.15 cM region. Pilot studies of randomly selected genomic regions
can be used to fine-tune the values of the ibdtrim parameter.

AUTHOR

       Beagle was written by Brian L. Browning.

       This manual page was written by Dylan Aïssi <bob.dybian@gmail.com>, for the Debian project
       (but may be used by others).

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

SEE ALSO

AUTHOR