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== STEP 6 : Run GotCloud Association Analysis Pipeline (EPACTS) ==
== STEP 6 : Run GotCloud Association Analysis Pipeline (EPACTS) ==
If you need to install EPACTS, please refer to the documentation at [[EPACTS#Installation_Details]]
We will assume that the EPACTS are installed in the following directory
setenv EPACTS /path/to/epacts
(If you need to install EPACTS, please refer to the documentation at [[EPACTS#Installation_Details]])
$EPACTS/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped \\
$EPACTS/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped \\
