Question

Best Variation Analysis Software which can support VCF file Format?

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10.1 years ago

Abdul Rafay Khan ★ 1.2k

I have data in vcf file format from ion torrent, I want to know which is the best Variation Analysis Software out there in market..

VCF SNP ngs variation • 7.0k views

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Abdul Rafay Khan ★ 1.2k

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Define "best Variation Analysis"

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Pierre Lindenbaum 164k

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I have .vcf files which i downloaded from ion torrent server, I want to analysis those files

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Abdul Rafay Khan ★ 1.2k

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Pierre understood your question perfectly. He was asking how you define 'best', what would your criteria be?

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by User 59 13k

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Gatk by Broad Institute

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by thiagomafra ▴ 70

Ram · Answer 1 · 2014-10-20

Have a look at Ensembl VEP, the Variant Effect Predictor. As the name says VEP predicts the effect of your variants on a given genome (whether it's deleterious or not; whether it falls in regulatory regions or not). The input data can be in VCF (plus many others). There is an online version of it (watch the tutorial video) in addition to a standalone Perl script and the REST API. It's worth having a look at the BioStars post by my colleague Emily.