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How to narrow down the variants after VQSR in germline variant discovery and filtering?

theomarkertheomarker qingdaoMember
edited April 2018 in Ask the GATK team

Hi GATK team,
I followd the gatk best practice for germline variant detection based on 100 WES samples. After VQSR, I got a VCF file, which is 39G in size (Actually, I think it seems too much). However, the other company offers me a text 430 thousands variants (snv + indel) after filtering. Since I am not sure how they processed or filter variants, can anyone tell me how to filter, refine and annotate to get a analysis ready VCF?

Best,
Jiahuan

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