SAMtools
We used the bcftools v1.9 utility from SAMtools to call SNPs on the
offspring and parent samples as a cohort. Filtering was performed by
removing sites with less than 20 quality score, genotype calls with less
than 5 depth, and then applying the set of common filters (Table 1). The
-G flag was set to the default (i.e., all samples were treated as one
population).