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, 10:22, 19 September 2012
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| M AGE | | M AGE |
| </pre> | | </pre> |
− | == 4. Run EPACTS association pipeline == | + | == 4. Run EPACTS association pipeline == |
| | | |
− | The basic EPACTS command for single variant tests is: | + | The basic EPACTS command for single variant tests is: |
− | <pre>perl epacts.pl single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.score -pheno DISEASE -cov AGE -sepchr -anno -run 10 | + | <pre>perl epacts.pl single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10 |
− | </pre> | + | </pre> |
− | This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. The VCF files are separated by chromosomes (hence the option -sepchr). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). | + | This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. The VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). |
| | | |
− | To run the Firth test as well, use: | + | To run the Firth test as well, use: |
| <pre>perl epacts.pl single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10 | | <pre>perl epacts.pl single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10 |
− | </pre> | + | </pre> |
− | For detailed description of options, use: | + | For detailed description of options, use: |
| <pre>perl epacts.pl single -man | | <pre>perl epacts.pl single -man |
− | </pre> | + | </pre> |
| <br> | | <br> |