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?
There are several options: I list you a couple that just came to my mind.

The most rigorous one would be to use [Mendel][1]. Method 9 is pedigree selection. Basically you specify all the possible pedigrees and it tells you which one is the most likely. Cons of this approach: 1) I am not sure it is easy to specify you data structure (one trio plus 14 unrelated males) to the software. You might have to do several comparisons between trios where mom-pup are the same and dad is changing. 2) I do not think mendel takes vcf as input.

Another approach would be to use the number of Mendelian inconsistencies to find the most probable father, using for example the [mendelian plugin][2] (I never tried it. For sure GATK has something similar). Basically, you run it on all the possible trios, i.e. for each mum-pup couple you rotate all the possible dads. If the dads are not related to the mom, then one of them (the real one) should show a sensibly lower number of mendelian inconsistencies. 

Be advised that either analysis you perform, you should perform it on a very reliable set of SNPs.


  [1]: https://www.genetics.ucla.edu/software/Mendel_current_doc.pdf
  [2]: https://samtools.github.io/bcftools/howtos/plugin.mendelian.html