<p>I wrote vcf2table: <a href="http://lindenb.github.io/jvarkit/VcfToTable.html" rel="nofollow noreferrer">http://lindenb.github.io/jvarkit/VcfToTable.html</a></p>
<pre><code>bcftools view in.bcf |  java -jar dist/vcf2table.jar | more
</code></pre>
<p><a href="https://i.sstatic.net/9Tc4w.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/9Tc4w.png" alt="enter image description here" /></a></p>
<p>and <a href="http://lindenb.github.io/jvarkit/SwingVcfView.html" rel="nofollow noreferrer">http://lindenb.github.io/jvarkit/SwingVcfView.html</a></p>
<p><a href="https://i.sstatic.net/UVKJ7.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/UVKJ7.png" alt="enter image description here" /></a></p>
<pre><code>java -jar dist/swingvcfview.jar indexed.vcf.gz
</code></pre>

CC BY-SA 4.0
2022-01-11T16:28:58.827Z
2022-01-11T16:28:58.827Z
Pierre
<p>OK it's a command line program, not a GUI, but <code>bcftools query</code> and <code>bcftools view</code> can easily be used to to view elements of a vcf/bcf file and are (probably) a lot more flexible and scalable than a GUI. Examples from <a href="https://samtools.github.io/bcftools/howtos/query.html" rel="nofollow noreferrer">here</a>:</p>
<pre><code>$ bcftools query -f '%CHROM %POS %REF %ALT\n' file.bcf | head -3
1 13380 C G
1 16071 G A
1 16141 C T
</code></pre>
<pre><code>$ bcftools query -f '%CHROM %POS  GTs:[ %GT]\t PLs:[ %PL]\n' file.bcf | head -3
1 10234  GTs: 1/1 1/1    PLs: 28,3,0 29,3,0
1 10291  GTs: ./. 1/1    PLs: 0,0,0 28,3,0
1 14907  GTs: 0/1 0/1    PLs: 8,0,17 26,0,48
</code></pre>

CC BY-SA 4.0
2022-01-06T20:32:52.860Z
2022-01-06T20:32:52.860Z
user438383
<p>Does anyone know a good, free-to-use VCF file inspector app (Mac OS, with GUI) where I can browse the content of a VCF file <a href="https://mybiosoftware.com/bamseek-20110724-browse-large-bam-sam-alignment-files.html" rel="nofollow noreferrer">similarly to bamseek</a>*?</p>
<p>I would like to browse SNP annotation split by columns, possibly even filter it.</p>
<p>'* Bamseek does not work for me, fails at open file. It anyways seems to be an abandonware.</p>
<p>Example table view from an expensive commercial software:
<a href="https://i.sstatic.net/yzAwe.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/yzAwe.png" alt="enter image description here" /></a></p>

<vcf><snp>
VCF file inspector app with GUI
# VCF file inspector app with GUI

(Asked by: username_0 on 2022-01-06)

Does anyone know a good, free-to-use VCF file inspector app (Mac OS, with GUI) where I can browse the content of a VCF file [similarly to bamseek](https://mybiosoftware.com/bamseek-20110724-browse-large-bam-sam-alignment-files.html)\*?

I would like to browse SNP annotation split by columns, possibly even filter it.

'\* Bamseek does not work for me, fails at open file. It anyways seems to be an abandonware.

Example table view from an expensive commercial software:
[![enter image description here](https://i.sstatic.net/yzAwe.png)](https://i.sstatic.net/yzAwe.png)

**Tags:** vcf, snp

---

## 2 answers

### Answer by username_1 on 2022-01-11. Score: 1 | Accepted answer

I wrote vcf2table: http://lindenb.github.io/jvarkit/VcfToTable.html
bcftools view in.bcf |  java -jar dist/vcf2table.jar | more


and http://lindenb.github.io/jvarkit/SwingVcfView.html

java -jar dist/swingvcfview.jar indexed.vcf.gz


---

### Answer by username_2 on 2022-01-06. Score: 2

OK it's a command line program, not a GUI, but bcftools query and bcftools view can easily be used to to view elements of a vcf/bcf file and are (probably) a lot more flexible and scalable than a GUI. Examples from here:
$ bcftools query -f '%CHROM %POS %REF %ALT\n' file.bcf | head -3
1 13380 C G
1 16071 G A
1 16141 C T

$ bcftools query -f '%CHROM %POS  GTs:[ %GT]\t PLs:[ %PL]\n' file.bcf | head -3
1 10234  GTs: 1/1 1/1    PLs: 28,3,0 29,3,0
1 10291  GTs: ./. 1/1    PLs: 0,0,0 28,3,0
1 14907  GTs: 0/1 0/1    PLs: 8,0,17 26,0,48


---

