Difference between revisions of "Test EPACTS for DIAGRAM"

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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  =
+
= Accessing help =
 +
 
 +
For a list of commands available in EPACTS, type in the following commands:
 +
<pre>'''$ 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
 +
 
 +
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
 +
 
 +
...
 +
 
 +
 
 +
</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:  
−
<pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
+
<pre>$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
  
−
${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped
+
$ 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:  
−
<pre>${EPACTS_DIR}/epacts single \
+
<pre>$ epacts2/epacts single \
−
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
+
--vcf epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
−
--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped \
+
--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>  
−
 
+
<pre>
−
= 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>

Revision as of 17:12, 26 September 2012

Download EPACTS

EPACTS is available for download here (100Mb) .

Requirements

  • Linux 64bit
  • Perl 5

Install EPACTS

Uncompress EPACTS package to the directory you would like to install 

 tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz

Accessing help

For a list of commands available in EPACTS, type in the following commands: 

'''$ 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

To view options for single variant testing only type in:
$ 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

...

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: 

$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

$ epacts2/example/1000G_dummy_pheno.ped


Run the single variant score test on the example data using this command: 

$ epacts2/epacts single \
--vcf epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
--ped epacts2/example/1000G_dummy_pheno.ped \
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
--out {OUTPUT_DIR}/test --run 2 &

This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001.  The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX.  The output file directory prefix is {OUTPUT_DIR}/test.  Finally, EPACTS will run the analysis in parallel on 2 CPUs.

Expected output

EPACTS produces a number of files and plots.

1.  test.epacts.gz contains all the association results. 

> head test.epacts
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA
20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA
20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA
20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA
20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA
20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA
20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587

2.  test.epacts.top5000 contains the top 5000 associated variants ordered by p-value. 

$ head out/test.single.b.score.epacts.top5000 
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681
20 4162411 4162411 20:4162411_T/C_Intron:SMOX 266 204 1 0.38346 0.00055585 -3.4523
20 34061918 34061918 20:34061918_T/C_Intron:CEP250 266 39 1 0.073308 0.0011231 3.2577
20 4155948 4155948 20:4155948_G/A_Intron:SMOX 266 215 1 0.40414 0.0020791 -3.0787
20 4680251 4680251 20:4680251_A/G_Nonsynonymous:PRNP 266 186 1 0.34962 0.0025962 3.0119
20 36668874 36668874 20:36668874_G/A_Synonymous:RPRD1B 266 96 1 0.18045 0.003031 2.9646
20 36641871 36641871 20:36641871_G/A_Synonymous:TTI1 266 10 1 0.018797 0.004308 -2.8547
20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313
20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822

3.  test.epacts.qq.pdf contains the Q-Q plot of test p-values (stratified by MAF)
Test b score epacts qq.png

4.  test.epacts.mh.pdf contains the Manhattan Plot of test p-values
The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.

Test b score epacts mh.png

An example Genome-wide manhattan plot (from a genome-wide run) will look like below

Tes b score epacts mh gw.png 

...
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