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Strategy low coverage ancient DNA- HaplotypeCaller
Has any staff member attempted to process low coverage ancient DNA (avg coverage <1) with low endogenous content using HaplotypeCaller. If so, what settings are suggested so as to minimize reference bias at very low coverage loci.
I am not sure if HaplotypeCaller can compete with callers specifically designed to deal with ancient DNA. Perhaps it can, I personally have not conducted comparison tests. Haak, 2015 suggested a random draw method.