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Test EPACTS for DIAGRAM (view source)

Revision as of 17:12, 26 September 2012

1,418 bytes removed ,  17:12, 26 September 2012
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   tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz
 
   tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz
   −
= Example  =
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= Accessing help =
 +
 
 +
For a list of commands available in EPACTS, type in the following commands:
 +
<pre>'''$ epacts2/epacts help'''
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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
 +
 
 +
To view options for single variant testing only type in:</pre><pre>$ 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
 +
 
 +
...
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 +
 
 +
</pre>
 +
= Getting started in EPACTS with an example =
    
Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
 
Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
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<pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
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<pre>$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
   −
${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped
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$ epacts2/example/1000G_dummy_pheno.ped
 
</pre>  
 
</pre>  
 
<br> Run the single variant score test on the example data using this command:  
 
<br> Run the single variant score test on the example data using this command:  
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<pre>${EPACTS_DIR}/epacts single \
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<pre>$ epacts2/epacts single \
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--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
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--vcf epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
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--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped \
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--ped epacts2/example/1000G_dummy_pheno.ped \
 
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
 
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
 
--out {OUTPUT_DIR}/test --run 2 &amp;
 
--out {OUTPUT_DIR}/test --run 2 &amp;
Line 68: Line 100:     
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>  
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<pre>
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= Additional options =
  −
 
  −
Type in the following command to view additional options available in EPACTS.
  −
<pre>&gt; /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>&gt; /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>
 
...</pre>
Clement Ma
216

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