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I am walking myself through the suggested variant call analysis flowthrough and have noticed that in various steps (e.g. UnifiedGenotyper and VariantRecalibrator), one should provide vcf files containing known SNPs.
In the case of UnifiedGenotyper, I assume that omitting the --dbSNP option and adding -contamination dbSNPs,vcf would allow me to keep only unknown (possible RNA-editing) variants.
I am also at loss on how to deal with the above problem in the case of VariantCallRecalibrator and other possible steps downstream UnifiedGenotyper necessary to efficiently obtain high quality variants.