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, 17:15, 24 September 2012
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− | == 1. Download and install EPACTS ==
| + | # Download EPACTS |
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| 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]. |
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− | If you want to use EPACTS in an Ubuntu platform, following the step below
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− | * Download EPACTS binary at http://www.sph.umich.edu/csg/kang/epacts/download/epacts2.noref_binary.2012_07_03.tar.gz (94MB) | + | Requirements |
− | * Uncompress EPACTS package to the directory you would like to install | + | |
| + | *Linux (e.g. Ubuntu) |
| + | *Perl vX |
| + | *gcc vX |
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| + | |
| + | # 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 |
− | * Download the reference FASTA files by running the following commands
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− | cd epacts2/
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− | ./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)
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− | * Perform a test run by running the following command
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− | example/test_run_epacts.sh
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− | | + | # Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are: |
− | Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are: | |
| <pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | | <pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz |
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| --out {OUTPUT_DIR}/test --run 2 & | | --out {OUTPUT_DIR}/test --run 2 & |
| </pre> | | </pre> |
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| 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. |