Example script to run CRAFT-GP pipeline

run_craft_gp_example.sh

#!/bin/bash
#
# Run example CRAFT-GP pipeline based on docs
#
# 0. Set up test data
if [ ! -d test-data ] ; then
    mkdir test-data
fi
cat >test-data/test_index_snps.in <<EOF
rs	chr	position
rs2301888	1	17672730
rs28411352	1	38278579
rs12140275	1	38633879
EOF
cat >test-data/test_summary_stats.in <<EOF
SNPID      CHROM  POS       A1  A2  A1_UNAFF  PVAL
rs6823274   4     26098057  G   A   0.1484    0.4064
rs76632663  2     43568820  T   G   0.06988   0.4427
rs28719598  8     10943884  T   C   0.194     0.7702
rs78519860  6     128145388 T   C   0.07869   0.9007
EOF
#
# 1. Define regions
echo "### Running define_regions_main.rb ###"
ruby scripts/define_regions_main.rb -i test-data/test_index_snps.in -m 0.1
#
# 2. Credible SNPs
echo "### Running filter_summary_stats.py ###"
python scripts/filter_summary_stats.py \
       --regions output/regions/region_boundaries_01cm.txt \
       --stats test-data/test_summary_stats.in \
       --out gwas_summary.subset
echo "### Running credible_snps_main.R ###"
Rscript --vanilla scripts/credible_snps_main.R \
	-r output/regions/region_boundaries_01cm.txt \
	-a 1962 \
	-u 8923 \
	-s gwas_summary.subset
##
#