how to use existed database to filter snps in vcf with MAF

Question

[jiangpeng59]

I am reading a research paper that uses GATK to call variants and filtration.

Annotated variants were subsequently filtered to exclude the variants greater or equal to 1% of minor allele frequency based on dbSNP135 and the 1000 genome project and the NHLBI Exome Variant server (EVS). "

I get two questions:

1. Where can I down load the right database?

2. Is there a convenient tools to filter variants with these databse?

many thanks !

Answer 1

[jared.andrews07]

1. This is multiple databases. 1000 Genomes has many releases, as does dbSNP (v135 is like 7 years old at this point). Those links will provide a starting point, but you'll likely have to search around and google for the exact releases you want.

2. VEP is probably the most common tool that checks the 1000 genomes VAF for SNPs in dbSNP. This page will likely provide some help, and the documentation is pretty thorough. VEP also has provides a lot of other info, like predicted consequence on protein structure or regulatory activity, etc. annovar and snpEff are other popular options that work quite well for variant annotation. Read up on them to see if they provide what you want.