How to visualize large VCF files

Question

[bioinforesearchquestions]

Dear all,

Is there any tool to visualize large VCF file in windows or linux?

[liangjiao.xue]

You could visualize VCF files in https://www.broadinstitute.org/igv/

The VCF can be zipped and indexed using tabix

bgzip       BIG.vcf   
tabix -p vcf BIG.vcf.gz

[bioinforesearchquestions]

Thanks Liangjiao for providing me the details. I really appreciate it. I will check and update you.

Answer 1

[Denise CS]

If your data is on any of the Ensembl species or from our sister project Ensembl Genomes, you can visualise your VCF files in our browser. More details can be found here. Your VCF needs to be compressed and indexed. Watch this video for more details. This is how a VCF would like. Once the VCF is attached you will get the annotation of the variants based on SO consequence terms. See this example.

[bioinforesearchquestions]

Thanks Denise for your reply. I really appreciate it. I couldn't see the virus genomes. But I also work on the human and mouse genome. So it will be a great help for me. I will go through the links you provided.

[Denise CS]

No viral genomes in Ensembl Genomes. Check their FAQ.