Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-21T11:10:55.837Z
Answers.LastActivityDate: 2017-06-21T11:10:55.837Z
Answers.UserDisplayName: Alex Reynolds
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-21T11:16:36.923Z
Comments.Text: Please show us an example of your inputs. What format are your SNPs in? Are they in a proper VCF file? Are they in some other format one per line? Many per line? Do you want a command line solution? an online graphical tool? Please [edit] your question and clarify.
Comments.UserDisplayName: terdon
Tags: <snp>
Title: Find gene at position from gff or gbk file
ThreadText: # Find gene at position from gff or gbk file
  
  (Asked by: username_0 on 2017-06-21)
  
  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?
  
  **Tags:** snp
  
  > **Comments:**
  > **username_1**: Please show us an example of your inputs. What format are your SNPs in? Are they in a proper VCF file? Are they in some other format one per line? Many per line? Do you want a command line solution? an online graphical tool? Please [edit] your question and clarify.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-06-21. Score: 3 | Accepted answer
  
  Via [BEDOPS](https://github.com/bedops/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
  
  ```
  
  
  ---
  
  