<p>If you want to filter a VCF file, you might want to give <strong>VCFtools</strong> a try.</p>

<p>Here is the documentation : <a href="http://vcftools.sourceforge.net/man_latest.html" rel="nofollow noreferrer">VCFtools Manual</a></p>

<p>I am not a specialist of this tool but you could do as the following. First build a bedfile with the chromosome names and positions of your genes (start and stop) such as this :</p>

<pre><code>chr   start   stop   (name)   (score)   (strand)
</code></pre>

<p>Then it should work with this command line :</p>

<pre><code>vcftools --vcf file.vcf --bed positions.bed --out filtered.vcf
</code></pre>

<p>The output will be a VCF filtered on the provided regions</p>

CC BY-SA 4.0
2020-01-06T16:08:21.030Z
thanks, I will try that!
user6720
CC BY-SA 4.0
2020-01-06T09:59:52.677Z
2020-01-06T09:59:52.677Z
Paul Endymion
<p>I have a <code>.vcf</code> file generated using <code>samtools</code>. I want to know mutations in specific genes by comparing <code>.vcf</code> files with a reference genome. I cannot use the Ensembl VEP tool as my reference genome is not listed there. Can you please help?</p>

CC BY-SA 4.0
2020-01-06T09:58:52.010Z
Using SnpEff (http://snpeff.sourceforge.net/SnpEff_manual.html#databases) you can build custom annotation databases using the gff or gtf file. VEP also offers similar functionality https://asia.ensembl.org/info/docs/tools/vep/script/vep_custom.html.
arup
<vcf>
bedtool intersect to compare .vcf file to reference genome
# bedtool intersect to compare .vcf file to reference genome

(Asked by: username_0 on 2020-01-06)

I have a `.vcf` file generated using `samtools`. I want to know mutations in specific genes by comparing `.vcf` files with a reference genome. I cannot use the Ensembl VEP tool as my reference genome is not listed there. Can you please help?

**Tags:** vcf
> **Comments:**
> **username_1**: Using SnpEff (http://snpeff.sourceforge.net/SnpEff_manual.html#databases) you can build custom annotation databases using the gff or gtf file. VEP also offers similar functionality https://asia.ensembl.org/info/docs/tools/vep/script/vep_custom.html.  

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## 1 answers

### Answer by username_2 on 2020-01-06. Score: 1

If you want to filter a VCF file, you might want to give VCFtools a try.
Here is the documentation : VCFtools Manual
I am not a specialist of this tool but you could do as the following. First build a bedfile with the chromosome names and positions of your genes (start and stop) such as this :
chr   start   stop   (name)   (score)   (strand)

Then it should work with this command line :
vcftools --vcf file.vcf --bed positions.bed --out filtered.vcf

The output will be a VCF filtered on the provided regions

> **Comments:**
> **username_0**: thanks, I will try that!  

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