UNIX for Dummies Questions & Answers

chr1    10001980    T    A

1    chr1    41980    41981    snp    A    G    dbsnp.86:rs806721

#!/bin/bash
while read line
do
    col1=$(echo $line | awk '{print $1}')
    col2=$(echo $line | awk '{print $2}')
    row_from_file2=$(grep " $col1 " file2 | grep " $col2 ")
    file2_col2=$(echo $row_from_file2 | awk '{print $2}')
    file2_col4=$(echo $row_from_file2 | awk '{print $4}')
    if [[ "$col1" = "$file2_col2" && "$col2" = "$file2_col4" ]]
    then
        echo "Found a match"
        echo "$line $row_from_file2" >> file3
    fi
done < file1

# cat file1
chr1 10001980 T A
# cat file2
1 chr1 41980 41981 snp A G dbsnp.86:rs806721
1 chr1 41980 10001980 snp A G dbsnp.86:rs806721
# ./match_file1_file2.bash
Found a match
# cat file3
chr1 10001980 T A 1 chr1 41980 10001980 snp A G dbsnp.86:rs806721

nawk 'FNR==NR{f1[$1,$2]=$0;next}{idx=$2 SUBSEP $4; if(idx in f1) $0=f1[idx] OFS $0}1' file1 file2