hg38.awk

#!/usr/bin/awk -f

NR == FNR && FNR == 1 {
    headers = $0
    empty_row = ""
    for (i = 0; i < NF; i++) {
        empty_row = "\t-" empty_row
    }
    next
}

# In file2 where we found hg38
# We transform "hg38:Chr11:8823729," to "chr11:8823729"
# And use that as a key in the array `found`
NR == FNR && $4 ~ /^hg38:/ {
    extra = $4
    sub(/hg38:/, "", extra)
    sub(/Chr/, "chr", extra)
    sub(/,$/, "", extra)
    found[extra] = $0
}

# First line of file1
# Print the existing headers and an additional column
NR != FNR && FNR == 1 {
    print $0 "\t" headers
    next
}

# Subsequent lines of file1
NR != FNR {
    printf $0
    key = $1 ":" $2
    if (key in found) {
        print "\t" found[key]
    } else {
        print empty_row
    }
}