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).