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?
You can use VAT in the VAAST pipeline to annotate mutations.
A brief description of this variant annotation tool and several others are included in the tools section: http://www.biostars.org/show/tools/
You have done a very nice job in the tools section.
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
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