file1
3 1234581 A C rs123456
file2 zipped file .gz
1 1256781 rs987656 T C
3 1234581 rs123456 A C
22 1792471 rs928376 G T
output
3 1234581 rs123456 A C
I tried
zcat file2.gz | awk 'NR==FNR{a[$1,$2,$5]++;next} a[$1,$2,$3]' file1.txt - > output.txt
but it is not working
Please try following
awk
code for your shown samples. Usezcat
to read your .gz file and then pass it as 2nd input toawk
program for reading, after its done reading with file1.Fixes in OP's attempt: