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== STEP 4 : EPACTS association analysis ==
== STEP 4 : EPACTS association analysis ==
In addition to variant calls, we need phenotype information to perform association mapping. Here, the phenotypes are created so that case is enriched in the individuals carrying rare nonsynonymous variants at CFTR.
% less ${GC}/examples/index/chr7.CFTR.ped
#FAM_ID IND_ID DAD_ID MOM_ID SEX PHENO QT
NA06984 NA06984 0 0 0 1 -0.657149296617419
NA06985 NA06985 0 0 0 2 -0.449034856685281
NA06986 NA06986 0 0 0 1 0.0975849179986626
NA06989 NA06989 0 0 0 2 1.77095069670763
NA06994 NA06994 0 0 0 1 0.287475900193007
NA07000 NA07000 0 0 0 1 -1.36632872407691
NA07037 NA07037 0 0 0 2 -0.1278913321612
NA07048 NA07048 0 0 0 2 -1.45798868745693
NA07051 NA07051 0 0 0 1 -0.599618650565132
...
Create a directory to store association results
% mkdir assoc
% mkdir assoc
% time ${GC}/epacts/bin/epacts single --ped ${GC}/examples/index/chr7.CFTR.ped --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out assoc/single.b.score --test b.score --anno --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
Run single variant logistic score test.
% ${GC}/epacts/bin/epacts single --ped ${GC}/examples/index/chr7.CFTR.ped --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out assoc/single.b.score --test b.score --anno --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
% time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa
% time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa
