text: user223: I have a VCF file with SNPs from a bacterial genome and want to find if the SNPs are located inside genes, is there some CLI-tool where you can pass a VCF file and a gff or gbk file and it returns the name of the genes?
  
  user776: Via BEDOPS:
  $ gff2bed < annotations.gff > annotations.bed
  $ vcf2bed < snps.vcf > snps.bed
  $ bedmap --echo --echo-map-id-uniq snps.bed annotations.bed > answer.bed
  
  This can be reduced to a one-liner if you're using bash:
  $ bedmap --echo --echo-map-id-uniq <(vcf2bed < snps.vcf) <(gff2bed < annotations.gff) > answer.bed
  
  
original_text: 223: <p>I have a VCF file with SNPs from a bacterial genome and want to find if the SNPs are located inside genes, is there some CLI-tool where you can pass a VCF file and a gff or gbk file and it returns the name of the genes?</p>
   776: <p>Via <a href="https://github.com/bedops/bedops" rel="nofollow noreferrer">BEDOPS</a>:</p>
  
  <pre><code>$ gff2bed &lt; annotations.gff &gt; annotations.bed
  $ vcf2bed &lt; snps.vcf &gt; snps.bed
  $ bedmap --echo --echo-map-id-uniq snps.bed annotations.bed &gt; answer.bed
  </code></pre>
  
  <p>This can be reduced to a one-liner if you're using <code>bash</code>:</p>
  
  <pre><code>$ bedmap --echo --echo-map-id-uniq &lt;(vcf2bed &lt; snps.vcf) &lt;(gff2bed &lt; annotations.gff) &gt; answer.bed
  </code></pre>
  