How to visualize large VCF files
1
0
Entering edit mode
8.2 years ago

Dear all,

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

VCF variant calling SNPS SNP variant • 5.6k views
ADD COMMENT
1
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
8.2 years ago
Denise CS ★ 5.2k

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.

ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

No viral genomes in Ensembl Genomes. Check their FAQ.

ADD REPLY

Login before adding your answer.

Traffic: 2479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6