==GeneABEL==
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name Aff --transpose --recode --out gwa_gabel --noweb
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name systolic --transpose --recode --out gwa_gabel_qtl --noweb
==Imputation exercise==
plink --file chr22_imputation_ex --noweb
plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check --noweb
names(dosage)
plot(dosage$BP, -log10(dosage$P))
dosagep = dosage[which(dosage$P < 5E-8),] dosagep = dosagep[order(dosagep$BP),] dosagep
interest = dosage[which(dosage$SNP=='rs715586'),]
interest
gws_unadj = aff_unadj[which(aff_unadj$P < 0.0000001),]
gws_unadj
gws_adjusted = aff_C1C2[which(aff_C1C2$P < 0.0000001),] gws_adjusted
q()
pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask include="DP>14" geno=DP:ge:11 file=YRI hwe=5.7e-7:1 "mac=1 maf=0.01" loc.group=refseq > SKAT_YRI.result
head -20 SKAT_YRI.result
cat SKAT_YRI.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15==RV-TDT exercise==
==RV-TDT exercise==
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
# clean
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
==SEQPower==
spower -h
spower LOGIT -h
==Unphased==
unphased.sh
unphased mypeds.ped –marker 1 2 3 –missing –permutation 10
==VAT==
vtools -h
vtools init VATDemo