There's even more complications to complicate the complications ... "you need many reads to get consensus even for any individual base" Not necessarily. If y

There's even more complications to complicate the complications ... "you need many reads to get consensus even for any individual base" Not necessarily. If you know that the minor allele frequency it close to 50% in related populations and you only have a few reads, say 6, and three are minor allele non reference and three are "major" allele reference (and the quality is good and there's otherwise low regional noise), then it's a good bet it's HETEROZYGOUS. You don't necessarily need a lot of reads. "second, you have to deal with the fact that a human genome has two copies of any individual chromosome" Well. Sort of. Men only have one Y chromosome and one X chromosome for instance, women have zero Y's. (a nitpick, granted). Disease sample often have 0,1 and 3 or more copies of a genomic area.