Question: How to find (count) location/type of variant from a VCF file ?
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gravatar for pinninti1991reddy
2.2 years ago by
pinninti1991reddy50 wrote:

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 ?

snp • 1.3k views
ADD COMMENTlink written 2.2 years ago by pinninti1991reddy50
1

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 REPLYlink modified 2.2 years ago • written 2.2 years ago by Nandini840

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 REPLYlink written 2.2 years ago by pinninti1991reddy50

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 REPLYlink written 2.2 years ago by Nandini840
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