filter and annotate vcf file

Question

[arwa.ahmad95]

I want to annotate and filter my vcf file using allele frequency ( <0.02 ) and quality (pass) using bcftools. this is the datasets that I use it : refGene,exac03,esp6500siv2_all,gnomad_exome,clinvar_20210501,dbscsnv11,dbnsfp42a How ? I'm newer in the field.

[abedkurdi10]

First, you have to annotate your VCF files with one of the know annotation tools like snpEff, Annovar, VEP, and then you can easily filter out variants based on your thresholds.

[arwa.ahmad95]

I download ANNOVAR and the databases I want it but I don't know how I annotate using ANNOVAR can you help me please!

[Sean Davis]

What errors are you getting when you follow the Annovar documentation? Be sure to post the commands that you are using.