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, 02:31, 7 January 2014
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| The slides describing the notes below are available [[Media:Stom practice 08.pdf | here (PDF)]] | | The slides describing the notes below are available [[Media:Stom practice 08.pdf | here (PDF)]] |
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| + | Updated version is available at https://www.dropbox.com/s/uhyjnqugovvbw6a/stom_practice_08.pdf |
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| === Basic Setup === | | === Basic Setup === |
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| cat ~/out/assoc/group.skat.o.epacts | cut -f 4,6,10,11 | | cat ~/out/assoc/group.skat.o.epacts | cut -f 4,6,10,11 |
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− | $S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2
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| * Run Variable Threshold test | | * Run Variable Threshold test |
| $S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2 | | $S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2 |
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− | * cat ~/out/assoc/group.VT.epacts | cut -f 4,6,10,13 | + | cat ~/out/assoc/group.VT.epacts | cut -f 4,6,10,13 |