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?
I recently came across [Peddy][1] that I'll be trying out soon. [VCF tools][2] also has a couple of implementations in `--relatedness` and `--relatedness2`, which are based on Yang et al, and Manichaikul et al respectively. There's also [KING][3] which I think was used in ExAC. 


  [1]: https://github.com/brentp/peddy
  [2]: https://vcftools.github.io/man_latest.html
  [3]: http://people.virginia.edu/~wc9c/KING/manual.html