Difference between revisions of "Test EPACTS for DIAGRAM"

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== Expected output  ==
 
== Expected output  ==
 +
 +
EPACTS produces a number of files and plots.
 +
 +
#'''test.epacts.gz''' contains all the association results.
 +
<pre>&gt; 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
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 +
</pre>
 +
#'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
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<pre>&gt; tail test.epacts.top5000
 +
20 56090807 56090807 20:56090807_A/G_Synonymous:CTCFL 266 112 1 0.21053 0.99754 -0.0030785
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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
 +
 +
</pre>
 +
#'''test.epacts.qq.pdf''' is the QQ-plot by MAF bin.
  
 
<br>
 
<br>

Revision as of 21:22, 24 September 2012

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.

  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
  1. 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
  1. test.epacts.qq.pdf is the QQ-plot by MAF bin.


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