title: How can I compare 3 files together (to see what is in common between them)?
body: <p>I want to compare 3 files together to see how much of the information in the files are the same. The file format is something like this:</p>
  
  <pre><code>Chr11   447     .       A       C       74      .       DP=22;AF1=1;CI95=1,1;DP4=0,0,9,8;MQ=15;FQ=-78   GT:PL:GQ        1/1:107,51,0:99
  Chr10   449     .       G       C       35      .       DP=26;AF1=0.5;CI95=0.5,0.5;DP4=5,0,7,8;MQ=20;FQ=11.3;PV4=0.055,0.0083,0.028,1   GT:PL:GQ        0/1:65,0,38:41
  Chr12   517     .       G       A       222     .       DP=122;AF1=1;CI95=1,1;DP4=0,0,77,40;MQ=23;FQ=-282       GT:PL:GQ        1/1:255,255,0:99
  Chr10   761     .       G       A       41      .       DP=93;AF1=0.5;CI95=0.5,0.5;DP4=11,34,6,35;MQ=19;FQ=44;PV4=0.29,1.8e-35,1,1      GT:PL:GQ        0/1:71,0,116:74
  </code></pre>
  
  <p>I'm only interested in the first two columns (if the first two columns are the same then I consider it as equal). This is the comand that I use for comparing two files :</p>
  
  <pre><code>awk 'FILENAME==ARGV[1] {pair[$1 " " $2]; next} ($1 " " $2 in pair)'  file1 file2 | wc -l
  </code></pre>
  
  <p>I would like to use the awk command since my files are really big and awk handle them really good! but I couldn't figure out how to use it for 3 files!</p>