Question

What web services can annotate and postprocess a complete human genome VCF coming from Illumina Tru-seq machine?

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6.9 years ago

mathisdead ▴ 10

What web services can annotate and postprocess a human genome VCF coming from Illumina Tru-seq machine? Have a whole genome SNP/indel discovery VCF from the Illumina. Young adult patient has a medullary thyroid cancer. Looking for a proper tools to annotate and postprocess it to build good reports and plots. Thx.

vcf illumina annotation postprocessing • 1.5k views

ADD COMMENT • link updated 6.9 years ago by andrew ▴ 560 • written 6.9 years ago by mathisdead ▴ 10

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a whole human genome VCF ? a faster solution is to download the tool (snpeff, vep) and to run it locally...

ADD REPLY • link 6.9 years ago by Pierre Lindenbaum 165k

score 0 · Answer 1 · 2018-03-14

I work for this company, so I am biased. iVariantGuide is an easy to use web-based tool that takes VCFs as input (4.1 or higher) and will annotate the file and provide graphical filtering and visualizations. It also can produce pathway enrichment analysis, GO analysis, and can produce an automated written summary. Currently the application has an unlimited trial, but some features are locked unless you get a subscription. It supports, single sample, paired sample, trios, and case-control multi-sample VCFs. Give it a try.

Here's a brief video describing the application.