ip_3_merge_bed_files.sh

#!/bin/bash
set -e

source constants_.sh
source parse_args.sh "$@"
source parse_chrs.sh
eval $(parse_chrs $chrs)

if [[ -z ${imp} ]]; then echo "imp argument is missing!"; exit 1; fi
if [[ -z ${target} ]]; then echo "target argument is missing!"; exit 1; fi
if [[ -z ${threads} ]]; then threads=22; fi
if [[ -z ${chrs_range} ]]; then chrs_range=($(seq 1 22)); fi

target_path=${datasets_path}${target}"/${imp}/"

echo 'About to merge bed files'
rm ${target_path}/raw/impute2/bed/mergelist.txt || echo ""
for i in "${chrs_range[@]}"; do
    echo ${target_path}/raw/impute2/bed/ds$i >> ${target_path}/raw/impute2/bed/mergelist.txt  
done
plink --merge-list ${target_path}/raw/impute2/bed/mergelist.txt --make-bed --out ${target_path}/raw/impute2/bed/ds.all || ret=$?

if [[ -f ${target_path}raw/impute2/bed/ds.all-merge.missnp ]] && [[ ret -ne 0  ]]; then
    echo 'Merge failed, probably due to inconsistent snps. About ot remove those SNPs'
    for i in "${chrs_range[@]}"; do
        plink --bfile ${target_path}/raw/impute2/bed/ds$i \
        --exclude ${target_path}raw/impute2/bed/ds.all-merge.missnp \
        --make-bed --out ${target_path}/raw/impute2/bed/ds${i}.fixed || echo ""

        mv ${target_path}/raw/impute2/bed/ds${i}.fixed.fam ${target_path}/raw/impute2/bed/ds${i}.fam
        mv ${target_path}/raw/impute2/bed/ds${i}.fixed.bim ${target_path}/raw/impute2/bed/ds${i}.bim
        mv ${target_path}/raw/impute2/bed/ds${i}.fixed.bed ${target_path}/raw/impute2/bed/ds${i}.bed
    done

echo "Retrying to merge (fixed) chrs files"
    plink --exclude ${target_path}/raw/impute2/bed/ds.all-merge.missnp \
    --merge-list ${target_path}/raw/impute2/bed/mergelist.txt \
    --make-bed --out ${target_path}/raw/impute2/bed/ds.all
fi