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I have an inbred mouse strain that I am sequencing and there should be little to NO heterozygosity. Yet with the default settings of UGT -heterozygosity (which is 0.001) many homs are being called as hets. When 230/250 reads are alternate and 20/250 are reference, it calls a het, even though it should be homozygous alternate.
What do you recommendations for this setting for inbred animals?
thanks, GATK is great!