Test EPACTS for DIAGRAM: Difference between revisions
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Created page with '== 1. Download and install EPACTS == EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here]. If you want to use EPACTS in a…' |
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# Download EPACTS | |||
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here]. | EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here]. | ||
* | Requirements | ||
* Uncompress EPACTS package to the directory you would like to install | |||
*Linux (e.g. Ubuntu) | |||
*Perl vX | |||
*gcc vX | |||
# Install EPACTS | |||
Uncompress EPACTS package to the directory you would like to install | |||
tar xzvf epacts2.noref_binary.2012_07_03.tar.gz | tar xzvf epacts2.noref_binary.2012_07_03.tar.gz | ||
# 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>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | <pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | ||
| Line 26: | Line 28: | ||
--out {OUTPUT_DIR}/test --run 2 & | --out {OUTPUT_DIR}/test --run 2 & | ||
</pre> | </pre> | ||
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. | 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. | ||
Revision as of 17:15, 24 September 2012
- Download EPACTS
EPACTS is available for download here.
Requirements
- Linux (e.g. Ubuntu)
- Perl vX
- gcc vX
- Install EPACTS
Uncompress EPACTS package to the directory you would like to install
tar xzvf epacts2.noref_binary.2012_07_03.tar.gz
- 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.
