Hi all,

I would like to filter / annotate my VCF and/or BAM files using dbSNP as part of the input during the steps of the variant calling workflow (other than the base recalibration step), are there any steps along the workflow where one can do so?

Or are you using Annovar or a similar program for that once you have a filtered VCF file?

Our workflow is based on the following: http://www.htslib.org/workflow/#mapping_to_variant

In addition to the variant caller mentioned there we also use FreeBayes & GATK for variant calling.

Thank you!
HI,

You can use [SnpEff][1] to annotate and [SnpSift][2] to filter variants using dbSNP.

Some useful information [here][3] (example 5).

 [1]: http://snpeff.sourceforge.net/
 [2]: http://snpeff.sourceforge.net/SnpSift.html
 [3]: http://snpeff.sourceforge.net/protocol.html#exFilter