<p>I'd advise against using <code>grep</code>, <code>sed</code>, <code>awk</code> for processing vcfs unless you really know what you're doing - there's almost always an easier way using <code>bcftools</code>.</p>
<p><code>bcftools view -i'ID=@snplist.txt' in.vcf</code></p>

CC BY-SA 4.0
2022-01-27T12:12:00.847Z
2022-01-27T12:12:00.847Z
user438383
<p>I have a vcf file containing an ID field with a snps and a list of human SNPs from dbSNP.I want to remove whatever in dbSNP from vcf file. The text file is like this:</p>
<pre><code>rs978760828
rs1008829651
rs1052373574
rs1326880612
rs768019142
rs892501864
rs1010989343
rs1489251879
rs1022805358
rs1322538365
</code></pre>
<p>How to remove the common snps from dbSNP and my vcf?</p>

<vcf><snp><bcftools>
Filtering a vcf with a text file of SNP rsIDs
# Filtering a vcf with a text file of SNP rsIDs

(Asked by: username_0 on 2022-01-27)

I have a vcf file containing an ID field with a snps and a list of human SNPs from dbSNP.I want to remove whatever in dbSNP from vcf file. The text file is like this:
rs978760828
rs1008829651
rs1052373574
rs1326880612
rs768019142
rs892501864
rs1010989343
rs1489251879
rs1022805358
rs1322538365

How to remove the common snps from dbSNP and my vcf?

**Tags:** vcf, snp, bcftools

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## 1 answers

### Answer by username_1 on 2022-01-27. Score: 1 | Accepted answer

I'd advise against using `grep`, `sed`, `awk` for processing vcfs unless you really know what you're doing - there's almost always an easier way using `bcftools`.

`bcftools view -i'ID=@snplist.txt' in.vcf`


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