SNP lookup with ld proxies

snp_lookup.R

# In R:

load("/panfs/panasas01/shared/alspac/deprecated/gib/aries_renormalised/condanal_results.RData")
mprobes <- c("cg06500161", "cg11024682", "cg07094298", "cg04011474", "cg10192877", "cg17782974", "cg20496314", "cg07202479", "cg09494176", "cg17501210", "cg21139312", "cg26403843") 

b <- subset(condres, CPG %in% mprobes)

write.table(unique(b$SNP), file="~/snplist.txt", row=F, col=F, qu=F)

snp_lookup.sh

# In Terminal:

# This is the summary stats for the most recent GWAS on BMI
bmifile="/projects/MRC-IEU/publicdata/GWAS_summary_data/GIANT_2014_2015/BMI2015/All_ancestries_SNP_gwas_mc_merge_nogc.tbl.uniq.gz"
zcat ${bmifile} | wc -l

# Find all rows that have the snp names in snplist.txt
zfgrep -wf snplist.txt ${bmifile} > foundsnps.txt
wc -l foundsnps.txt

# None found!

# Get LD proxies:
plink1.90 \
	--bfile /panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/2015-10-30/data/derived/filtered/bestguess/maf0.01_info0.8/combined/data \
	--show-tags snplist.txt \
	--list-all \
	--out snptags

# Try again with new snplilst
zfgrep -wf snptags.tags ${bmifile} > foundsnps.txt
zcat ${bmifile} | head -n 1 > header 
cat header foundsnps.txt