Question

Checking Frameshifts And Stop Codons In Gene

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11.7 years ago

bioinfo ▴ 830

I have a vcf file of my Snps and another vcf file for my indels produced by BWA and GATK. Is there any commands in vcftools or any other way I can find out the frameshifts due to indels/snps and produced stop codons due to snps in my genes?

snp vcftools • 4.1k views

ADD COMMENT • link updated 11.7 years ago by Christian ★ 3.0k • written 11.7 years ago by bioinfo ▴ 830

score 3 · Answer 1 · 2012-08-19

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11.7 years ago

Zev.Kronenberg 12k

You can use VAT in the VAAST pipeline to annotate mutations.

ADD COMMENT • link 11.7 years ago by Zev.Kronenberg 12k

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A brief description of this variant annotation tool and several others are included in the tools section: http://www.biostars.org/show/tools/

ADD REPLY • link 11.7 years ago by Malachi Griffith 19k

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You have done a very nice job in the tools section.

ADD REPLY • link 11.7 years ago by Zev.Kronenberg 12k

score 1 · Answer 2 · 2012-11-02

There are many variant annotation tools available for this job. The more popular ones that come to my mind are Ensembl's Variant Effect Predictor (VEP), ANNOVAR, SnpEff, or Sequent Variant Analyzer (SVA).

You could also use our own tool, CooVar, which was just published. Its easy to use and does not depend on external databases. So it's ideal if you work on a non-model organism.

CooVar: Co-occurring variant analyzer

BMC Research Notes 2012, 5:615