UnifiedGenotyper
We used GATK v3.8 UnifiedGenotyper to call SNPs separately in both the offspring samples and the parental sample. As with HaplotypeCaller, because VQSR was not applicable, we filtered using the hard-filter expression (https://gatk.broadinstitute.org/hc/en-us/articles/360035532412?id=11097), further filtered sites with less than 30 quality score, and then filtered using the common set of filters (Table 1).