Variant training set for Zebrafish to apply GATK VariantRecalibrator
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4.0 years ago
Matthias ▴ 50

I am working genotyping-by-sequencing data of Zebrafish and it seems that there is no training/truth variant set available for applying GATK Variant Quality Score Recalibration (VQSR). I only found the dbSNP vcf files.

Has anyone performed VQSR on Zebrafish data and/or can suggest a good variant set for training/validation?

I am thinking of creating my own test datasets filtering variants using the evidence status (http://www.ensembl.org/info/genome/variation/prediction/variant_quality.html). Has anyone experience with this?

SNP Zebrafish GATK Genotyping-by-sequencing NGS • 1.0k views
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