test.subs

#!/bin/bash
# 23-2-2017 MRC-Epid JHZ

chr=$1
trait=$2
rt=$3
rt2=$4

awk=/bin/awk
join=/usr/bin/join
python=/usr/local/Cluster-Apps/python/2.7.5/bin/python
gunzip=/bin/gunzip
sort=/bin/sort

# double the effort but easier for GNU parallel

cd $rt2/QUS
$gunzip -c $rt/refpanel/1kg_phase3_chr${chr}_eur_5pct_legend.txt.gz | \
$awk '{print chr,$1,sprintf("%00000000015d",$2),$2,$3,$4}' chr=$chr | $sort -k3 > $chr

# Step 0 - GWAS summary statistics

echo $trait-$chr
$awk 'NR>1' ${trait}.${chr}.txt | \
$awk '{$2=sprintf("%00000000015d",$2);print}' | $sort -k2 > $trait-$chr
$join -13 -22 $chr $trait-$chr | $awk -f $rt2/test.awk > ${trait}-${chr}.dat

# Step 1 - compute eigenvalues and projections

$python $rt/hess.py \
  --chrom $chr \
  --h2g $trait-$chr.dat \
  --reference-panel $rt/refpanel/1kg_phase3_chr${chr}_eur_5pct_gen.txt.gz \
  --legend-file $rt/refpanel/1kg_phase3_chr${chr}_eur_5pct_legend.txt.gz \
  --partition-file $rt/nygcresearch-ldetect-data-ac125e47bf7f/EUR/fourier_ls-chr${chr}.bed \
  --out $trait