We'd like to perform trio analysis of mice to detect de novo mutations (via WGS and variant calling). The complication: our mouse facility performs breeding in bulk (~15 each males and females). Mom-pup pairs are obviously straightforward. To identify dads, our strategy is to sequence all of the males and infer paternal parentage by comparing dad-pup SNPs. One method is to manually identify SNPs at heterozygous loci for discrimination, but I assume there are tools that can perform this analysis from bulk VCFs. Any suggestions?