__NOTITLE__
==ANNOVAR COMMANDS==
table_annovar.pl
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Gene.vcf -remove -nastring . -protocol refGene -operation g -vcfinput
cat APOC3_Gene.vcf.hg19_multianno.txt
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Gene.vcf -remove -nastring . -protocol refGene,knownGene,ensGene -operation g,g,g -arg '-splicing
12 -exonicsplicing','-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing' -vcfinput
awk -F'\t' '{print $1,$2,$6,$7,$8,$9,$10}' APOC3_Gene.vcf.hg19_multianno.txt
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Region.vcf -remove -nastring . -protocol phastConsElements46way -operation r -vcfinput
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Region.vcf -remove -nastring . -protocol gwasCatalog -operation r -vcfinput
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Filter.vcf -remove -nastring . -protocol
gnomad_genome,gnomad_exome,popfreq_max_20150413,gme,avsnp150,dbnsfp33a,dbscsnv11,cadd13gt20,clinvar_20170905,gwava -operation f,f,f,f,f,f,f,f,f,f -vcfinput
awk -F'\t' '{print $1,$2,$103,$104}' APOC3_Filter.vcf.hg19_multianno.txt
awk -F'\t' '{print $1,$2,$6,$14}' APOC3_Filter.vcf.hg19_multianno.txt
awk -F'\t' '{print $1,$2,$15,$16,$17,$18,$19,$20,$21,$22}' APOC3_Filter.vcf.hg19_multianno.txt
awk -F'\t' '{print $1,$2,$36,$86,$70}' APOC3_Filter.vcf.hg19_multianno.txt
awk -F'\t' '{print $1,$2,$99,$100}' APOC3_Filter.vcf.hg19_multianno.txt
table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_ANN.vcf -remove -nastring . -protocol
refGene,knownGene,ensGene,wgRna,targetScanS,phastConsElements46way,tfbsConsSites,gwasCatalog,gnomad_genome,gnomad_exome,popfreq_max_20150413,gme,avsnp150,dbnsfp33a,dbscsnv11,cadd13gt20,clinvar_20170905,gwava -operation g,g,g,r,r,r,r,r,f,f,f,f,f,f,f,f,f,f -arg '-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing',,,,,,,,,,,,,,, -vcfinput
==GeneABEL==
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name Aff --transpose --recode --out gwa_gabel --noweb
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name systolic --transpose --recode --out gwa_gabel_qtl --noweb
descriptives.scan(test.eg)
snp.eg <- row.names(results(test.eg))[results(test.eg)$P1df < alpha]
pvalue.eg <- results(test.eg)$P1df[results(test.eg)$P1df < alpha] lambda.eg <- test.eg@lambda snp.eg pvalue.eg lambda.eg
for (k in 1:10){
test.tmp <- egscore(disease, data = g.dat, kin = adj.gkin, naxes = k)
plot(test.qt, col = "black")
add.plot(test.eg, col = "gray", pch = 3)
legend("topright", c("Original plot","After correction w/ EIGENSTRAT"), pch = c(1,3))==GWAS Data QC==
==GWAS Data QC==
plink --file GWAS --noweb
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind --noweb
==VAT==
vtools -h
vtools init VATDemo