Max Alt Alleles behavior
I'm using HaplotypeCaller to call a vcf file with 8 samples. I left the --max_Alt_Alleles argument at its default 6. However I'm getting some odd warning messages:
WARN 19:12:58,670 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr1:2274306 has 26 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
Since I'm calling 8 samples, shouldn't the maximum number of alternate alleles be 15 (2n-1)? Or is the number of alternate alleles observed in the given context referring to the number of possible haplotypes that could possibly be constructed from the aligned reads?