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Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 8 (view source)
Revision as of 01:33, 7 January 2014
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$S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf $S5/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
$S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf $S5/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
* Look at your score
* Look at the association statistics
head = ~/out/assoc/single.b.score.epacts.top5000
head = ~/out/assoc/single.b.score.epacts.top5000
