Question: Filter/Annotate VCF with dbSNP during variant calling workflow
1
gravatar for alons
4.2 years ago by
alons270
Rehovot
alons270 wrote:

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!

dbsnp bam ngs vcf variant calling • 2.9k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 4.2 years ago by alons270
3
gravatar for Evgeniia Golovina
4.2 years ago by
New Zealand
Evgeniia Golovina990 wrote:

HI,

You can use SnpEff tool to annotate and SnpSift to filter variants using dbSNP.

Some useful information there (example 5).

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Evgeniia Golovina990
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