Test EPACTS for DIAGRAM
Download EPACTS
EPACTS is available for download here (100Mb) .
Requirements
- Linux 64bit
- Perl vX
- gcc vX
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
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:
${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped
Run the single variant score test on the example data using this command:
${EPACTS_DIR}/epacts single \
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
--ped {EPACTS_DIR}/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.
- 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
- test.epacts.top5000 contains the top 5000 associated variants ordered by p-value.
> tail test.epacts.top5000 20 56090807 56090807 20:56090807_A/G_Synonymous:CTCFL 266 112 1 0.21053 0.99754 -0.0030785 20 2560716 2560716 20:2560716_T/G_Intron:TMC2 266 68 1 0.12782 0.99755 -0.0030708 20 60885142 60885142 20:60885142_C/A_Normal_Splice_Site:LAMA5 266 215 1 0.40414 0.99757 0.0030423 20 11903654 11903654 20:11903654_G/A_Synonymous:BTBD3 266 20 1 0.037594 0.99777 -0.0027986 20 57768657 57768657 20:57768657_T/C_Synonymous:ZNF831 266 20 1 0.037594 0.99811 0.0023631 20 30037783 30037783 20:30037783_C/T_Intron:DEFB123 266 282 1 0.46992 0.99853 -0.0018438 20 61990878 61990878 20:61990878_C/T_Intron:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819 20 61990939 61990939 20:61990939_G/A_Synonymous:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819 20 13464030 13464030 20:13464030_C/A_Intron:TASP1 266 231 1 0.43421 0.99944 -0.00070181 20 60905717 60905717 20:60905717_T/C_Intron:LAMA5 266 471 1 0.11466 0.9995 0.00063136
$ 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
Q-Q plot of test statistics (stratified by MAF)
The file out/test.b.score.epacts.qq.pdf will be generated as shown below
Manhattan Plot of Test Statistics
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
