How to check the quality of VCF file for GWAS analysis

Question

[Qingyang Xiao]

I recently started a GWAS project. My previous colleagues have preprocessed the genotyping file and made the vcf file (each person, each variant).

What aspects can I check that if the files are qualitywise ready for GWAS analyses?

Thanks.

[Jeremy]

See the following post on filtering VCF files:

Criteria for Variant Call

Answer 1

[raphael.B]

Assuming you're processing WGS data:

Gatk provides a few answers with the VQSR score or their hard filters. But truth is you won't find a filter that works perfectly. My advice would be follow these standards that are quite permissive, and check a posteriori your hits on IGV (or equivalent) to make sure your variants are true positive.