Hi,
I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.
Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator
My question is how should I proceed if I have to select rare variants (MAF<1%) for the candidate genes that I have,for each of these 20 samples?
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written
by
Ron
1 answer
You can use 1000 genome and/or ESP frequencies to determine rare variants.
There are lots of tools to accomplish this, with ANNOVAR being one of the most popular:
http://www.openbioinformatics.org/annovar/
This software also has a web interface, called wANNOVAR:
SeattleSNP can also accomplish this:
http://snp.gs.washington.edu/SeattleSeqAnnotation138/
It is possible that you may need to reformat some files in order to get the variant annotation to work properly.
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