Test EPACTS for DIAGRAM

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_09_27.tar.gz

Download the reference FASTA files by running the following commands

cd epacts2.1/
./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)

Accessing help

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

$ epacts2.1/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
make-group Create the group information for gene-based testing
make-kin Create a kinship matrix

Visit http://genome.sph.umich.edu/wiki/EPACTS for more detailed documentation

To view options for single variant testing only type in:

$ epacts2.1/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:

$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

$ epacts2.1/example/1000G_dummy_pheno.ped

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

$ epacts2.1/epacts single \
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
--ped epacts2.1/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 {OUTPUT_DIR}/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 {OUTPUT_DIR}/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)

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.

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