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*?

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


2 Answers 2


I wrote vcf2table: http://lindenb.github.io/jvarkit/VcfToTable.html

bcftools view in.bcf |  java -jar dist/vcf2table.jar | more

enter image description here

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

enter image description here

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

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

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