==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
snp.data = dbp[,c("affection", "rs1112")]
summary(snp.data)
snp.data[,"rs1112"]<-as.numeric(snp.data[,"rs1112"])-1<br /> summary(snp.data)<br /> result.all=glm(affection ~ rs1112, family=binomial("logit"), data=snp.data)<br /> dev.all = anova(result.all, test="Chi")<br /> summary(result.all) print(dev.all)<br /> snp.data = dbp[,c("affection","trait","sex","age","rs1112","rs1117")]<br /> summary(snp.data)<br /> snp.data[,"rs1112"]<-as.numeric(snp.data[,"rs1112"])-1<br /> snp.data[,"rs1117"]<-as.numeric(snp.data[,"rs1117"])-1<br /> result.adj = glm(affection ~ sex + rs1112, family=binomial("logit"), data=snp.data)<br /> summary(result.adj)
result.adj = glm (affection ~ age + rs1112 , family=binomial("logit"), data=snp.data)
summary(result.adj)
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==
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
vtools phenotype --from_file data/phen.txt
# variant selection
vtools execute ANNOVAR geneanno
vtools select variant "variant.region_type like '%splicing%'or variant.mut_type like 'nonsynonymous%' or variant.mut_type like 'frameshift%' or variant.mut_type like 'stop%'" -t func_variant
# tped file
vtools export func_variant --format tped --samples 'phenotype is not null' > vat_raw.tped
sort -k4 -n vat_raw.tped | awk 'BEGIN{OFS="\t";prev="None";copy=1} {$2=$1"_"$4; $3=0; if($2==prev) {$2=$2"_"copy; copy=copy+1} else {prev=$2; copy=1}; print $0}' > vat_export.tped
# tfam file
vtools phenotype --out family sample_name pid mid sex phenotype > vat_export.tfam
# anno file
vtools use refGene-hg19_20130904
vtools update func_variant --set 'maf=0.001'
vtools select func_variant -o chr pos refGene.name2 maf --header > vat_export.anno
# Mendelian error and recode
plink --noweb --tfile vat_export --recode12 --me 1 1 --set-me-missing --out "recode12_noME"
sort -n -k1 -k6 -k2 recode12_noME.ped | sed 's/ /\t/g' | cut -f1,3,4,5 --complement > linkage.ped
cut -f2 recode12_noME.map | awk 'BEGIN{OFS="\t";} {print "M",$0}' | sed '1i\I\tid\nA\tDisease' > linkage.dat
java -Xmx10000m -jar java/linkage2beagle.jar linkage.dat linkage.ped > pre_beagle.bgl
python script/pre_phase.py -i pre_beagle.bgl -a pre_beagle_withMissing.bgl
java -Xmx10000m -jar java/beagle.jar missing=0 trios=pre_beagle.bgl out=bgl_phased verbose=false redundant=true
gunzip bgl_phased.pre_beagle.bgl.phased.gz
python script/post_phase.py -a vat_export.anno -b bgl_phased.pre_beagle.bgl.phased -o genes/
for g in `ls genes | grep tped | cut -d"." -f1 | head -20`
do
echo "runing rvTDT on gene "${g}
rvTDT exercise_proj -G ./genes/${g}.tped -P ./data/rvtdt.phen -M ./genes/${g}.map --adapt 500 --alpha 0.00001 --permut 2000 --lower_cutoff 0 --upper_cutoff 100 -- minVariants 3 --maxMissRatio 1
done
# Answer
vtools show tables
cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k2
cat exercise_proj_pval/*.pval | grep -v "^#" | sort -k3
# clean
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
==SEQPower==
spower -h
for i in 1 1.5 2 2.5 3 3.5 4; do
spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental $i --method "CFisher --name CMC$i" --title FixedOR$i -r 100 -j 4 -l 1 -o exercise2
done<br />spower show exercise2.SEQPowerDB LOGIT method power title ==Unphased==
unphased.sh
unphased mypeds.ped –marker 1 2 3 –missing –permutation 10
unphased mypeds.ped –window 2 –reference 1 2 1 1
unphased all.ped -window 2 -LD
unphased all.ped -window 2 -LD >> results.txt==VAT==
vtools -h
vtools init VATDemo