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The Unified Genotyper calls SNPs relative to the specified, publicly-available reference assembly.

How can I call SNPs (in many samples, with UG) relative to an in-house individual, which I have sequenced at high-coverage?

My current solution is to perform a de novo assembly on the in-house reference individual using e.g. Velvet, and then simply use the fasta as the reference for UG.

Can the publicly-available reference assembly still be useful here for speeding up the mapping and filling-in missing parts ?

My organism is Drosophila melanogaster.