VCF Combination.sh

sum_id=
for ID in $(ls | grep -P -o '.*(?=(.vcf$))')
#List all VCF files and Compress / Index
do
    echo Compress and index the ${ID}.vcf files
    if [ ! -f ${ID}.vcf.gz.tbi ] ;then
        if [ ! -f ${ID}.vcf.gz ] ;then
            bgzip ${ID}.vcf
            pids="$pids $!"
            wait $pids
        fi
        tabix -p vcf ${ID}.vcf.gz
        pids="$pids $!"
        wait $pids
    fi
done

for ID in $(ls | grep -P -o '.*(?=(\.vcf.gz$))')
# Get the ID files in list
do
    sum_id="$sum_id $ID"
done
echo $sum_id

echo Pick 2 in all IDs
set -- $sum_id
# Create ID sets
for a; do
    if [ "$#" -gt 0 ]; then shift; fi
    for b; do
        printf "%s - %s\n" "$a" "$b"
        bcftools isec -p ${a}_${b} ${a}.vcf.gz ${b}.vcf.gz
        pids="$pids $!"
        echo Finish intersection ${a}_${b}
        wait $pids
        if [ ! -d two_pair ] ;then
            mkdir two_pair
        fi
        cd ${a}_${b}
        mv 0002.vcf ../two_pair/${a}_${b}.vcf
        cd ..
        echo
        echo
    done
done

echo Compress and index the two_pair vcf files
cd two_pair
    for ID in $(ls | grep -P -o '.*(?=(.vcf$))')
    do
        if [ ! -f ${ID}.vcf.gz.tbi ] ;then
            if [ ! -f ${ID}.vcf.gz ] ;then
                echo Compress ${ID}.vcf
                bgzip ${ID}.vcf
                pids="$pids $!"
                wait $pids
            fi
            echo Index ${ID}.vcf
            tabix -p vcf ${ID}.vcf.gz
            pids="$pids $!"
            wait $pids
        fi
    done
cd ..

echo Pick 3 in all IDs
set -- $sum_id
for a; do
    if [ "$#" -gt 0 ]; then shift; fi
    for b; do
        if [ "$#" -gt 0 ]; then shift; fi
        for c; do
            printf "%s - %s - %s\n" "$a" "$b" "$c"
            bcftools isec -p ${a}_${b}_${c} two_pair/${a}_${b}.vcf.gz ${c}.vcf.gz
            pids="$pids $!"
            echo Finish intersection ${a}_${b}_${c}
            wait $pids
            if [ ! -d three_pair ] ;then
                mkdir three_pair
            fi
            cd ${a}_${b}_${c}
            mv 0002.vcf ../three_pair/${a}_${b}_${c}.vcf
            cd ..
            echo
            echo
        done
    done
done