Tagged with #vqsr non-model de-novo
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Created 2013-08-15 19:05:17 | Updated | Tags:
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Hello - how should I go about running VariantRecalibrator if I don't have any prior variant information for my organism? I assume I could use the same trick as for base quality recalibration - use the really confident SNPs from the pilot variant calling within the same dataset as a training set - but for some reason I cannot find how to convert my vcf file of those super-confident SNPs into the form that can be used fed into VariantRecalibrator. Cheers, Misha