text: user4595: 
  EDITED
  
  I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For example name of one vcf is LP6008031-DNA_A04_vs_LP6008032-DNA_D03.snp.pass.vcf
  OC/AH/120/E/T3  LP6005409-DNA_F01
  OC/AH/126/E/T1  LP2000325-DNA_A01
  OC/AH/136/E/T3  LP6005409-DNA_E02
  
  This is the link of my file https://www.dropbox.com/s/mvzf47feiqe7x69/clin_name.txt.txt?dl=0
  In the second file name pre_post.list I have information of pre or post treatment for each sample like this
  pre-treated post-treated
  OC/AH/120   OC/AH/065
  OC/AH/126   OC/AH/069
  OC/AH/136   OC/AH/074
  OC/AH/160   OC/AH/084
  
  This is link of this https://www.dropbox.com/s/ikrl1h8yoc0sngx/pre_post.list.xlsx?dl=0
  As you suggested I typed 
  cat pre_post.list | awk '{print $2}' | sed 's@.*/@@'  > post_list.txt
  cat pre_post.list | awk '{print $1}' | sed 's@.*/@@'  > pre_list.txt
  
  Then I have 
  pre-treated
  120
  126
  136
  160
  182
  
  post-treated
  065
  069
  074
  084
  
  in I typed ./test.sh in which I wrote
  for item in  $(cat  pre_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $item clin_name.txt ;
      then out=$(grep $item clin_name.txt | awk  '{print $1}');
           cp *$out* /temp/hgig/fi1d18/TRG45/snp/
      else echo post_list $item;  fi;  done;
  
  That returns
  cp: cannot stat `*OC/AH/069/S/T3*': No such file or directory
  [fi1d18@cyan01 snp]$
  
  Or I run 
  for item in  $(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $item clin_name.txt ;
      then out=$(grep $item clin_name.txt | awk  '{print $1}');
           cp *$out* /temp/hgig/fi1d18/TRG45/snp/pre/
      else cp *$out* /temp/hgig/fi1d18/TRG45/snp/post/;  fi;  done;
  
  That returns
  cp: cannot stat `OC/ST/026/S/T1*': No such file or directory
  [fi1d18@cyan01 snp]$
  
  I really don't know how to solve this :(
  
  user6487: Assuming the names of all the files from one group are in file named list.  
  cat pre_post.list | awk '{print $2}' | sed 's@.*/@@'  > post_list.txt
  cat pre_post.list | awk '{print $1}' | sed 's@.*/@@'  > pre_list.txt
  
  Now you have two number list
      for item in  $(cat  pre_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $item clin_name.txt ;
      then out=$(grep $item clin_name.txt | awk  '{print $1}');
           cp *$out* /dir/for_pre_files/
      else echo post_list $item;  fi;  done
  
  for post
      for item in  $(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $item clin_name.txt ;
      then out=$(grep $item clin_name.txt | awk  '{print $1}');
           cp *$out* /dir/for_post_file/
      else echo Prelist $item;  fi;  done
  
  or you could do this if one that isn't in post belongs in pre
      for item in  $(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $item clin_name.txt ;
      then out=$(grep $item clin_name.txt | awk  '{print $1}');
           cp *$out* /dir/for_post_file/
      else cp *$out* /dir/for_pre_file/;  fi;  done
  
  
original_text: 4595: <blockquote>
    <p>EDITED</p>
  </blockquote>
  
  <p>I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name <code>clin_name.txt</code> like below. For example name of one vcf is <code>LP6008031-DNA_A04_vs_LP6008032-DNA_D03.snp.pass.vcf</code></p>
  
  <pre><code>OC/AH/120/E/T3  LP6005409-DNA_F01
  OC/AH/126/E/T1  LP2000325-DNA_A01
  OC/AH/136/E/T3  LP6005409-DNA_E02
  </code></pre>
  
  <p>This is the link of my file <a href="https://www.dropbox.com/s/mvzf47feiqe7x69/clin_name.txt.txt?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/mvzf47feiqe7x69/clin_name.txt.txt?dl=0</a></p>
  
  <p>In the second file name <code>pre_post.list</code> I have information of pre or post treatment for each sample like this</p>
  
  <pre><code>pre-treated post-treated
  OC/AH/120   OC/AH/065
  OC/AH/126   OC/AH/069
  OC/AH/136   OC/AH/074
  OC/AH/160   OC/AH/084
  </code></pre>
  
  <p>This is link of this <a href="https://www.dropbox.com/s/ikrl1h8yoc0sngx/pre_post.list.xlsx?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/ikrl1h8yoc0sngx/pre_post.list.xlsx?dl=0</a></p>
  
  <p>As you suggested I typed </p>
  
  <pre><code>cat pre_post.list | awk '{print <span class="math-container">$2}' | sed 's@.*/@@'  &gt; post_list.txt
  cat pre_post.list | awk '{print $</span>1}' | sed 's@.*/@@'  &gt; pre_list.txt
  </code></pre>
  
  <p>Then I have </p>
  
  <pre><code>pre-treated
  120
  126
  136
  160
  182
  
  post-treated
  065
  069
  074
  084
  </code></pre>
  
  <p>in I typed <code>./test.sh</code> in which I wrote</p>
  
  <pre><code>for item in  <span class="math-container">$(cat  pre_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $</span>item clin_name.txt ;
      then out=<span class="math-container">$(grep $</span>item clin_name.txt | awk  '{print <span class="math-container">$1}');
           cp *$</span>out* /temp/hgig/fi1d18/TRG45/snp/
      else echo post_list $item;  fi;  done;
  </code></pre>
  
  <p>That returns</p>
  
  <pre><code>cp: cannot stat `*OC/AH/069/S/T3*': No such file or directory
  [fi1d18@cyan01 snp]$
  </code></pre>
  
  <p>Or I run </p>
  
  <pre><code>for item in  <span class="math-container">$(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $</span>item clin_name.txt ;
      then out=<span class="math-container">$(grep $</span>item clin_name.txt | awk  '{print <span class="math-container">$1}');
           cp *$</span>out* /temp/hgig/fi1d18/TRG45/snp/pre/
      else cp *$out* /temp/hgig/fi1d18/TRG45/snp/post/;  fi;  done;
  </code></pre>
  
  <p>That returns</p>
  
  <pre><code>cp: cannot stat `OC/ST/026/S/T1*': No such file or directory
  [fi1d18@cyan01 snp]$
  </code></pre>
  
  <p>I really don't know how to solve this :(</p>
   6487: <p>Assuming the names of all the files from one group are in file named list.  </p>
  
  <pre><code>cat pre_post.list | awk '{print <span class="math-container">$2}' | sed 's@.*/@@'  &gt; post_list.txt
  cat pre_post.list | awk '{print $</span>1}' | sed 's@.*/@@'  &gt; pre_list.txt
  </code></pre>
  
  <p>Now you have two number list</p>
  
  <pre><code>    for item in  <span class="math-container">$(cat  pre_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $</span>item clin_name.txt ;
      then out=<span class="math-container">$(grep $</span>item clin_name.txt | awk  '{print <span class="math-container">$1}');
           cp *$</span>out* /dir/for_pre_files/
      else echo post_list $item;  fi;  done
  </code></pre>
  
  <p>for post</p>
  
  <pre><code>    for item in  <span class="math-container">$(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $</span>item clin_name.txt ;
      then out=<span class="math-container">$(grep $</span>item clin_name.txt | awk  '{print <span class="math-container">$1}');
           cp *$</span>out* /dir/for_post_file/
      else echo Prelist $item;  fi;  done
  </code></pre>
  
  <p>or you could do this if one that isn't in post belongs in pre</p>
  
  <pre><code>    for item in  <span class="math-container">$(cat  post_list.txt | grep -Eo '[0-9]{1,4}');
      do if grep -q $</span>item clin_name.txt ;
      then out=<span class="math-container">$(grep $</span>item clin_name.txt | awk  '{print <span class="math-container">$1}');
           cp *$</span>out* /dir/for_post_file/
      else cp *$out* /dir/for_pre_file/;  fi;  done
  </code></pre>
  