Flags
|
Required/Optional
|
Description |
-h <file>
|
Required
|
A file containing a set of known
haplotypes. Each line of this
file should specify one haplotype. Each haplotype should be a sequence
of 1's and 0's that correspond to the alleles at each locus of the
haplotype. The length of each haplotype must be the same. For example,
the example input file (ex.haps)
contains 5 haplotypes at 10 SNPs. See the following section for links to the relevant HapMap
files.
|
-l <file>
|
Required |
A
legend file
for the SNP markers. This file should have 4 columns
with one line for each SNP. The columns should contain an ID for each
SNP i.e. rs id of the marker, the base pair position of each SNP, base
represented by 0 and base represented by 1. The first line of the
legend file are column labels (these are not used by the program but
the file is required to contain a header line). See the example file
ex.leg. See the following section for links to
the relevant HapMap files.
|
-r <file>
|
Optional
|
The
program can also
take a file containing the fine-scale recombination rate across the
region.
This file should have 3 columns with one line for each SNP. The columns
should
contain physical location, rate in cM/Mb to the right of the marker and
the
cumulative rate in cM to the left of the marker. A header line
containing
the column labels is required. See the example file ex.map. See the following section for links to the relevant HapMap
files.If
no recombination file is specified and the option -rho
(see below) is not used then the recombination rate between all loci is
set to 0.
|
| -n <int> <int> |
Recommended
|
Sets the number of control and
the number of case individuals to simulate. For example -n
100 100 simulates 100 control and 100 case individuals. The
default is to generate 1 control and 1 case individual. |
-gen
|
Optional |
Output files that contain
genotypes for each
individual. The files will have the suffix .g.
The genotypes will be given as one line per individual. The genotypes
will be coded 0,1 or 2. The genotypes will be given at the set of SNPs
specified by the user (see -t
option below). |
-snptest
|
Optional
|
Output files in the FILE
FORMAT used by IMPUTE, SNPTEST
and GTOOL. A separate genotype
and a sample file is written for cases and controls. The files
will have the suffices
.gen and .sample.The
genotypes will be given at the set of SNPs
specified by the user (see -t
option below). |
-hap
|
Optional
|
Output files that contain pairs
of haplotypes for each
individual. The files will have the suffix .h.
There will be one line for each
haplotype (pairs of conseutive lines contain the two haplotypes of each
individual). The haplotypes will be given as a sequence of 1's and 0's.
The haplotypes will be given at the set of SNPs
specified by the user (see -t
option below). |
-int <int> <int>
|
Optional
|
Specify the lower and upper
boundaries of the region in which you wish to carry out simulation.
|
| -o <file> |
Required
|
Output file prefix. For example -o
foo creates files foo.*
.The files that are produced depend upon the combination of the
flags -gen,
-hap, -snptest, -all and -t.
Output files not described elsewhere include
foo.y
- File containing the phenotype of each individual. The file has one
line for each indvidual and 1 and 0 are used to denote cases and
controls respectively. This file is only produced when the -gen
and -hap
flags are specified.
foo.aux
- File containing summaries of some of the parameters used in the
simulation. The file has the following format
disease
marker index
physical
position
minor
allele at disease locus
minor
allele frequency in haplotype set
heterozygous
relative risk
homozygous
relative risk
|
-t <file>
|
Optional |
SNP subset file. This option
allows the user to output data at only a subset of the SNP markers in
the simulated dataset i.e. at a set of tag SNPs. The file should
contain the physical location of markers that will be in the output on
one line per SNP. The physical locations must match those in the legend
file. If this option is selected then a
.tags output file will be
produced that contains the positions of the SNPs in the output file.
|
-all
|
Optional
|
Only relevant if the -t
option is used. In addition to the output files at the set of SNPs
selected by the -t
option a set of files at all SNPs will be produced. The additional
files will include .all.
in their names. If the -t option is not used then the -all option
is automatically turned on, thus producing files that contain data at
all SNPs.
|
-dl <int>
|
Optional
|
Sets disease locus location. For
example, -dl
1000 sets the disease locus to be the marker with physical
location 1000. Must be one of the locus in the legend file. If none is
given a random locus is chosen that satisfies the minor allele
frequency (MAF) range specified by the -freq
option below.
|
-freq <real> <real>
|
Optional
|
Sets min and max MAF for a
disease locus. Only relevant if no valid disease locus is specified
using the -dl
option. For example, -freq
0.1 0.3 sets the minimum and maximum MAF at the disease locus to
be 0.1 and 0.3. The default values are 0.05 and 0.5.
|
-rr <real> <real>
|
Optional |
Sets heterozygous and homozygous
relative risk. For example -rr
1.5 2.25 sets the heterozygous relative risk to 1.5 and
homozygous relative risk to 2.25. The default relative risk for
heterozygotes and homozygotes are both 1.0.
|
-flip
|
Optional |
Specifies that the major allele
will be
the disease allele. Minor allele is the disease allele by default.
|
| -Ne <int> |
Required if -r is used |
Sets effective population size
that scales the fine-scale recombination map for the given population.
For example, -Ne
11000
sets the effective population size to 11000. For autosomal chromosomes,
we highly recommend the values 11418 for CEPH, 17469 for Yoruban and
14269 for Chinese Japanese populations. |
-rho <real>
|
Optional |
Sets constant recombination rate
between all loci. Only relevant if no recombination rate file is given.
For example, -rho
10 sets the recombination rate between all loci to 10 cM/Mb and
this will then be scaled by the user supplied value of Ne. If -r
and -rho
are not used then the recombination rate is set to 0.
|
-theta <real>
|
Optional |
Sets mutation rate in the model.
For example, -theta
10 sets the scaled mutation rate to 10. Mutation rate is set to
that the expected number of mutations at a given SNP is equal to 1 by
default.
|
