Hello
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
thanks
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