text: user4595: I have a zipped vcf file of dbSNP hg38 version
  No space left on my device to unzip that
  I want to extract a column from that
  I have tried this
  cut -f 3 00-All.vcf.gz | sed 's/[\t]/,/g' > cols.csv
  
  But that needs my vcf to be unzipped
  Do you know any solution please?
  
  user3694: Either the zcat command or gunzip -c will decompress the file in a streaming fashion to the standard output without writing the decompressed data to disk. Pipe the output to cut, sed, etc.
  Try
  zcat 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' > cols.csv
  
  or
  gunzip -c 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' > cols.csv
  
  But if you just want a single 'column' (I presume you mean field), then you are better off just doing bcftools query.
  
original_text: 4595: <p>I have a zipped vcf file of dbSNP hg38 version</p>
  <p>No space left on my device to unzip that</p>
  <p>I want to extract a column from that</p>
  <p>I have tried this</p>
  <pre><code>cut -f 3 00-All.vcf.gz | sed 's/[\t]/,/g' &gt; cols.csv
  </code></pre>
  <p>But that needs my vcf to be unzipped</p>
  <p>Do you know any solution please?</p>
   3694: <p>Either the <code>zcat</code> command or <code>gunzip -c</code> will decompress the file in a streaming fashion to the standard output without writing the decompressed data to disk. Pipe the output to <code>cut</code>, <code>sed</code>, etc.</p>
  <p>Try</p>
  <pre><code>zcat 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' &gt; cols.csv
  </code></pre>
  <p>or</p>
  <pre><code>gunzip -c 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' &gt; cols.csv
  </code></pre>
  <p>But if you just want a single 'column' (I presume you mean field), then you are better off just doing <code>bcftools query</code>.</p>
  