text: user4595: I have a list of files in which I have this information
  Chrom   Position        Ref Alt TumorVAF    NormalVAF
  chr1    56987           CA  C   0.222222    0
  chr1    4133415         AG  A   0.425       0
  chr1    4611030         A   AC  0.36        0
  
  This is the name of one of my files
  LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf.parsed.txt
  
  I have another matched file which has too much information
  This is the name of these big files
  LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf_fixed_vcf.txt.hg19_multianno.txt
  
  As you are seeing, most of the name of txt files are matched
  I want to cut the 4th and 5th columns from my small files and add these columns to the matched big files
  Manually this is possible but time consuming for a lot of files
  Is these any way to do that by coding?
  
  user650: 
  As you are seeing, most of the name of txt files are matched
  
  Our eyes and brains are smarter than computers. We can see patterns that can be difficult to describe. For a computer to be useful in this task, the difference between the two file names must be explicitly defined.
  In your example (which seems to be an ANNOVAR-generated output file with a prefix specified during annovar run), the common part seems to be the output of $(basename LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf.parsed.txt .parsed.txt). If this is true for all files, you could automate that using a loop such as:
  for f in *.parsed.txt
  do
      other_file=$(basename "$f" .parsed.txt)
      # Rest of your logic goes here
  done
  
  You could then paste the columns from $f to $other_file like so (not tested):
  paste "$other_file" <(cut -f3,4 $f)
  
  This is an outline to get to your solution. You should be able to build off this.
  
original_text: 4595: <p>I have a list of files in which I have this information</p>
  
  <pre><code>Chrom   Position        Ref Alt TumorVAF    NormalVAF
  chr1    56987           CA  C   0.222222    0
  chr1    4133415         AG  A   0.425       0
  chr1    4611030         A   AC  0.36        0
  </code></pre>
  
  <p>This is the name of one of my files</p>
  
  <pre><code>LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf.parsed.txt
  </code></pre>
  
  <p>I have another matched file which has too much information</p>
  
  <p>This is the name of these big files</p>
  
  <pre><code>LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf_fixed_vcf.txt.hg19_multianno.txt
  </code></pre>
  
  <p>As you are seeing, most of the name of txt files are matched</p>
  
  <p>I want to cut the 4th and 5th columns from my small files and add these columns to the matched big files</p>
  
  <p>Manually this is possible but time consuming for a lot of files</p>
  
  <p>Is these any way to do that by coding?</p>
   650: <blockquote>
    <p>As you are seeing, most of the name of txt files are matched</p>
  </blockquote>
  
  <p>Our eyes and brains are smarter than computers. We can see patterns that can be difficult to describe. For a computer to be useful in this task, the difference between the two file names must be explicitly defined.</p>
  
  <p>In your example (which seems to be an ANNOVAR-generated output file with a prefix specified during annovar run), the common part seems to be the output of <code>$(basename LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf.parsed.txt .parsed.txt)</code>. If this is true for all files, you could automate that using a loop such as:</p>
  
  <pre><code>for f in *.parsed.txt
  do
      other_file=<span class="math-container">$(basename "$</span>f" .parsed.txt)
      # Rest of your logic goes here
  done
  </code></pre>
  
  <p>You could then <code>paste</code> the columns from <code>$f</code> to <code>$other_file</code> like so (not tested):</p>
  
  <pre><code>paste "<span class="math-container">$other_file" &lt;(cut -f3,4 $</span>f)
  </code></pre>
  
  <p>This is an outline to get to your solution. You should be able to build off this.</p>
  