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How to choose reference to calculate coverage of WGS of organism that has high intra-species variation?

Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation ...
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GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?

I'm looking for official GATK documentation (or a recent manuscript) that defines a general recommendation/requirement for sequencing depth to reliably call a heterozygous point mutation in a diploid ...