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Revision as of 13:47, 30 June 2014
, 13:47, 30 June 2014→Single Variant Association Analysis
Let's run a single-variant association analysis using a score test.
Let's run a single-variant association analysis using a score test.
$EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2
$EPACTS/bin/epacts-single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2
After running it, you will see EPACTS output files by looking at
After running it, you will see EPACTS output files by looking at
cat $OUT/assoc/emmax.epacts.top5000
cat $OUT/assoc/emmax.epacts.top5000
== Run Groupwise Test ==
== Run Groupwise Test ==
