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Revision as of 11:22, 10 July 2014
, 11:22, 10 July 2014→Run Groupwise Test
If you want to run a collapsing burden test (CMC), run the following command
If you want to run a collapsing burden test (CMC), run the following command
$EPACTS/bin/epacts group --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.collapse --test b.collapse --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
$EPACTS/bin/epacts group --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.collapse --test b.collapse --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
You can view the results by examining the output file
You can view the results by examining the output file
You can run SKAT-O test in a similar way, but with a special tag
You can run SKAT-O test in a similar way, but with a special tag
$EPACTS/bin/epacts group --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.skato --test skat --skat-o --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
$EPACTS/bin/epacts group --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.skato --test skat --skat-o --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
And view output files
And view output files
