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VariantRecalibrator (VQSR) without any training sets? (Simulated data)

afzmafzm Member
edited June 2018 in Ask the GATK team

How can I run VQSR in simulated variants data? In this dataset variants are randomly distributed along the genome so I can not use real truth vcf files. I have tried using the golden.vcf that the simulator produces but it says that it also needs annotation files, so what can I do?

Thank you

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