These are chat archives for dereneaton/ipyrad
max_alleles_consensis the maximum number of unique alleles allowed in (individual) consens reads. Different individuals can be biallelic at a site for different bases e.g. A/G vs A/T, which would give you this output in your vcf file (one ref and two alt alleles). Does this make sense?
filtered_by_rm_duplicatesissue, this is much more concerning. 72% filtered seems like theres a real issue. What is the reference sequence you're using?