FreeBayes
We used FreeBayes v1.3.1-17-gaa2ace8 to call SNPs separately in both the
offspring samples and the parental sample to account for the ploidy
difference. The resulting VCF files were merged using VCFtools. Genotype
calls with less than 20 genotype quality and/or less than 5 depth were
filtered out, before applying the set of common filters as described
above (Table 1).