I was wondering if there was anything available within galaxy that would let you do the following with pileup files:

1) filter for homozygous SNVs (i.e. that do not contain the reference genome allele in the genotype) 2) compare the pileup files for 2 (or more) individuals to find SNVs unique to each individual and to further limit this to homozygous SNPs unique to each individual 3) compare the pileup files for 2 (or more) individuals to find shared SNVs and to further limit to this to shared SNVs where the individuals have different alleles (rare as would assume triallelic snv) and then group the individuals according to the allele for each SNV.

I could only see the filter pileup tool but nothing for comparing pileup files

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