Question

Variant Annotation Integrator VCF File

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2.8 years ago

Riccardo ▴ 10

Hello everyone, I am trying to use the UCSC Variant Annotation Integrator tool. I have a vcf file generated from the SARS-CoV2 reference genome. Is it possible to directly upload the VCF file on the website or do I have to modify the file? Thanks in advance

vcf UCSC annotation • 731 views

ADD COMMENT • link updated 2.8 years ago by Luis Nassar ▴ 670 • written 2.8 years ago by Riccardo ▴ 10

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Hello Riccardo, click on add pgSnp or VCF custom track. At the right hand side of Paste URLs or data: click browse and choose your VCF file.

ADD REPLY • link 2.8 years ago by abedkurdi10 ▴ 190

score 0 · Answer 1 · 2022-02-23

Hello,

As posted before, on the Variant Annotation Integrator (http://genome.ucsc.edu/cgi-bin/hgVai) you can click on the "add pgSNP or VCF custom track" button:

add custom track

From there you can choose a local file to upload. Since it's a SARS-CoV2 vcf, upload should be fine. For very large VCFs you can also place on a web hosting location and provide just the URL.

If you have any follow up questions, our public help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.