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).