Difference between revisions of "Test EPACTS for DIAGRAM"
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| − | = Download | + | = Download EPACTS = |
| − | EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2_01.noref_binary.2012_07_06.tar.gz here (100Mb) ]. | + | EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2_01.noref_binary.2012_07_06.tar.gz here (100Mb) ]. |
| − | Requirements | + | Requirements |
| − | *Linux 64bit | + | *Linux 64bit |
| − | *Perl vX | + | *Perl vX |
*gcc vX | *gcc vX | ||
| − | = Install EPACTS = | + | = 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 | tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz | ||
| − | = Example = | + | = 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: | 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 27: | Line 29: | ||
--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. | ||
| − | + | == Expected output == | |
| − | + | <br> | |
| − | |||
Revision as of 21:07, 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
