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== STEP 6 : Run GotCloud Association Analysis Pipeline ==
== STEP 6 : Run GotCloud Association Analysis Pipeline ==
TBD/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped --out $GCOUT/epacts --test q.linear --run 1 --top 1 --chr 20
TBD/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped --out $GCOUT/epacts \\
--test q.linear --run 1 --top 1 --chr 20
Upon successful run, you will see files starting with $GCOUT/epacts
ls $GCOUT/epacts*
To see the top associated variants, you can run
less epacts.epacts.top5000
To see the (assuming GNU gnuplot 4.2 or higher version was installed), you can
xpdf EPACTS_TEST.zoom.20.42987877.pdf
= Tutorial Inputs =
= Tutorial Inputs =
