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[[Image:Test b score epacts mh.png]]
[[Image:Test b score epacts mh.png]]
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br> [[Image:Tes b score epacts mh gw.png]] <br>
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br> [[Image:Tes b score epacts mh gw.png]] <br>
= Additional options =
Type in the following command to view additional options available in EPACTS.
<pre>> /net/fantasia/home/hmkang/sw/epacts2/epacts help
Usage:
epacts [command] [options]
Command:
help Print out brief help message
man Print the full documentation in man page style
single Perform single variant association
group Perform groupwise (burden-style) association test
anno Annotate a VCF file
zoom Create a locus zoom plot from epacts results
meta Perform meta-analysis across multiple epacts results
Visit http://genome.sph.umich.edu/wiki/EPACTS for more detailed documentation
</pre>
To view options for single variant testing only type in:
<pre>> /net/fantasia/home/hmkang/sw/epacts2/epacts single -help
Usage:
epacts single [options]
Required Options (Run epacts single -man or see wiki for more info):
-vcf STR Input VCF file (tabixed and bgzipped)
-ped STR Input PED file for phenotypes and covariates
-out STR Prefix of output files
-test STR Statistical test to use
Key Options (Run epacts single -man or see wiki for more info):
-help Print out brief help message [OFF]
-man Print the full documentation in man page style [OFF]
-pheno STR Name of phenotype column from PED file [6th column]
-cov STR Name of covariate column(s) from PED file. []
-field STR VCF's FORMAT field of genotypes or dosages [GT]
-unit INT Base pair units for a parallel run [10000000]
-sepchr Indicator of separated VCF per chromosome [OFF]
-anno Annotate the results with functional category [OFF]
-run INT Run EPACTS immediately with specified # CPUs [0]
-min-maf FLT Minimum minor allele frequency [1e-6]
-min-callrate FLT Minimum call rate [0.5]
Other Options (Run epacts single -man or see wiki for more info):
-all-cov Use all possible covariates from PED file [OFF]
-chr STR Specific chromosome to run association []
-pass use only pass-filtered sites [OFF]
-info STR substring in the INFO field to be matched []
-kinf STR Kinship file if '-test q.oemmax' is used []
-kin-only Create kinship matrix only [OFF]
-inv-norm Inverse-normal transformation of phenotypes [OFF]
-restart Ignore intermediate results and restart [OFF]
-nodes STR Comma-separated list of MOSIX cluster nodes []
-missing STR String representing missing value [NA]
-noplot Skip producing the Manhattan and QQ plots [OFF]
-topzoom INT Produce locus zoom plot for top N signals [0]
...</pre>
