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It prints the line occurrence of column 1 ($1). a[$1]++ fails for the first occurrence increment since the array value for that key does not exist. The ! means not true so the expression is evaluated...

try:

sort -k9 -n -r file | awk '!a[$1]++'

In output shown above, what happened to the max line for chr1_17232_18061?

Can I add a word of caution that the lines in your exclude file will match anywhere on the line in your input file. If you need to ensure that it is (for example) only lines starting with abc then...

In this case go with RudiCs excellent suggestion: "-v" inverts the match, excluding the lines matching the pattern and "-f" reads the patterns from a file instead of arguments from the command line....

Then RudiC's suggestion should do what you want...
If the patterns in mylist are fixed strings, then:
grep -Fvf mylist file
will run a little bit faster. And, if the patterns are extended regular...

Did you consider using a pattern file:
grep -vf mylist file
This may not be the most efficient method, though.

How many different files are we talking about? This may work, but if there's more than 20 outputs or so, awk may choke from opening too many files:

awk '!($1 in A) { A[$1]="File" ++X } ; { print...

Using awk; reading input file twice:
awk '
NR == 1 {
print
}
NR == FNR && NR > 1 {
i = $2 FS $3 FS $4 FS $5
A[i] += $1
...

Hi,

Please use code tag for your input file, which help to make thread more readable.

Use below code for the desire o/p.

awk 'NR==FNR{a[$1]=$2;next}
a[$1]{print $0,a[$1];next}{print $0,"-...