homoplastic sites

[agmcarthur]

It would be interesting if the tree could label which positions are suspected of homoplasy: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473

[jts]

Cleaning up old issues, I think this is now out-of-scope

[raphenya]

@nodrogluap highlighted this might be worth re-opening see

• Repository: https://github.com/nodrogluap/pokay/tree/master/data and
• VCFs: https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/master/subset_vcf/problematic_sites_sarsCov2.mask.vcf