From Genome Analysis Wiki
Jump to navigationJump to search
38 bytes added
, 15:39, 26 October 2012
Line 40: |
Line 40: |
| | | |
| 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>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | + | <pre>$ epacts.v2.2.0.20121026/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz |
| | | |
− | $ epacts2.1/example/1000G_dummy_pheno.ped | + | $ epacts.v2.2.0.20121026/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>$ epacts2.1/epacts single | + | <pre>$ epacts.v2.2.0.20121026/epacts single |
| --vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz | | --vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz |
| --ped epacts2.1/example/1000G_dummy_pheno.ped | | --ped epacts2.1/example/1000G_dummy_pheno.ped |
Line 53: |
Line 53: |
| 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. |
| | | |
− | A more detailed description of the example can be found [http://genome.sph.umich.edu/wiki/Test_EPACTS_for_DIAGRAM here]. | + | A more detailed description of the example can be found [http://genome.sph.umich.edu/wiki/Test_EPACTS_for_DIAGRAM here]. |
| | | |
| == 2. Prepare VCF file with genotypes / dosages == | | == 2. Prepare VCF file with genotypes / dosages == |