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13291 NA06997 NA06986 NA07045 2 2 107.53 53.1
13291 NA06997 NA06986 NA07045 2 2 107.53 53.1
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The corresponding DAT file is:
The corresponding DAT file is:
<pre>M DISEASE
<pre>M DISEASE
M QT
M QT
M AGE
M AGE
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== 4. Run EPACTS association pipeline ==
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
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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).
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>
For detailed description of options, use:
<pre>perl epacts.pl single -man
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