I want to ask for opinions on dealing with non-uniquely mappable reads in pooled DNA sequencing.
Instead of sequencing individual samples, DNA from multiple samples are mixed and sequenced so as to identify variant and/or estimate allele frequencies. My question is, how do we properly handle non-uniquely mapped reads in this application? If they are discarded, it is almost certainly going to have bias in the estimation of allele frequency because one allele may be uniquely mappable and the other may be not. What would be the potential problem if such reads are assigned to a random alignment as BWA does?