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For users in CSG, EPACTS can be found here:
For users in CSG, EPACTS can be found here:
<pre>/net/fantasia/home/hmkang/sw/epacts2/</pre>
<pre>/net/fantasia/home/hmkang/sw/epacts2.1/</pre>
<br> 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:
<br> 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>$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
<pre>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
$ epacts2/example/1000G_dummy_pheno.ped
$ epacts2.1/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>$ epacts2/epacts single
<pre>$ epacts2.1/epacts single
--vcf epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
--ped epacts2/example/1000G_dummy_pheno.ped
--ped epacts2.1/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 &
--out {OUTPUT_DIR}/test --run 2 &
The basic EPACTS command for single variant tests is:
The basic EPACTS command for single variant tests is:
<pre>epacts2/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10
-test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10
</pre>
</pre>
To run the Firth test as well, use:
To run the Firth test as well, use:
<pre>epacts2/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10
</pre>
</pre>
For detailed description of options, use:
For detailed description of options, use:
<pre>epacts2/epacts.pl single -help
<pre>epacts2.1/epacts single -man
</pre>
</pre>
== 5. Report association results in appropriate format<br> ==
== 5. Report association results in appropriate format<br> ==
Once the EPACTS pipeline has completed, you will find all of the results in the ''.epacts ''file. Here is an example of score test results:
Once the EPACTS pipeline has completed, you will find all of the results in the ''.epacts.gz'' file. Here is an example of score test results:
<pre>#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
<pre>#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 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA
