How to find (count) location/type of variant from a VCF file ?

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6.3 years ago

pinn ▴ 210

Hi, I annotated VCF using Annovar, how to find different type/location of variants (Intergenic, Genic, CDS, Ts and Tv snps) ?

Can any one suggest me. Other then this is their a way to perform normalisation of an annotated VCF file ?

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ADD COMMENT • link 6.3 years ago by pinn ▴ 210

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If you have annotated the VCF file with annovar, your result/output file should already give you the different type/location of variants - that's generally what annotation tools do. If you want a detailed output, you can use VEP or SNPEff to annotate your file.

ADD REPLY • link 6.3 years ago by NB ▴ 960

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Hi Thanks for your response, Though file size is big I'm not able to sort it out in excel. Is their any scripts to classify the type of variants. Is their a way normalisation could be possible to remove False Positives (FP) and False Negatives (FN) snps ?

ADD REPLY • link 6.3 years ago by pinn ▴ 210

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Try SNPEff if you need the count for the different types of variants. It also generates a html page for easy view of your results. Regarding FP and FN variants, look here

ADD REPLY • link 6.3 years ago by NB ▴ 960

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