for file in /home/cmccabe/Desktop/concordance/comparison/update/*.txt ; do
    file1=${file##*/}    # Strip off directory
    getprefix=${file1%%_*.txt}
    file1=$(printf '%s\n' "/home/cmccabe/Desktop/concordance/reference/files/${file1%%_*.txt}_"*.txt) # look for matching file
    if [[ -f "$file1" ]]
    then
          awk '
BEGIN {FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 OFS $2 OFS $3] = $0
}
{for(i=1;i<=19;i++)
{if($i == "")$i = "."}
}
{if($2 OFS $4 OFS $5 in o)
o[$2 OFS $4 OFS $5] = $1 OFS $2 OFS $4 OFS $5 OFS $6 OFS $7 OFS $8 OFS $9 OFS $10 OFS $11 OFS $12 OFS $13 OFS $14 OFS $15 OFS $16 OFS $17 OFS $18 OFS $19           }   
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' $file $file1
   fi
done

awk: cmd. line:10: (FILENAME=/home/cmccabe/Desktop/concordance/comparison/update/F113.txt FNR=1) fatal: attempt to use array `i' in a scalar context

Missing in IDP but found in Reference:    
CHR    POS    REF    ALT    FUNC    GENE    COVERAGE    PHRED    A[#F,#R]    C[#F,#R]    G[#F,#R]    T[#F,#R]    INS[#F,#R]    DEL[#F,#R]    SNP    MUT    FREQ    SANGER    REGION
74992800    A    G    Not low     Not found
100794363    C    T    Not low     Not found
189931518    A    -    Not low     Not found