VarScan
We used VarScan v2.4.4 to call SNPs on the offspring data using a
p-value of 0.05 and no additional filters. We then called SNPs in the
parental sample in a similar manner and merged the resulting VCF files
using VCFtools. SNPs were filtered by removing sites with minor allele
frequencies below 0.10%, individual genotype calls with depths below
10, and then applying the common filters. As VarScan does not have a
ploidy setting (i.e., all genotype calls are diploid) and our offspring
sample data were haploid, we removed all heterozygote genotype calls
(Table 1).