Difference between revisions of "Test EPACTS for DIAGRAM"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 21: | Line 21: | ||
</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>${EPACTS_DIR}/epacts single | + | <pre>${EPACTS_DIR}/epacts single \ |
| − | --vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | + | --vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \ |
| − | --ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped | + | --ped {EPACTS_DIR}/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 & | ||
</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 17:20, 24 September 2012
Download EPACTS
EPACTS is available for download here (100Mb) .
Requirements
- Linux (e.g. Ubuntu)
- 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.
