Table 2.

Published and implemented filtering approaches for intrahost variants.

Approach	Sample Filters	Variant Filters
Valesano-like [44]	≥50,000 mapped reads ≥29,000 bp horizontal coverage	VAF ≥ 2%, VAF < 50% DP ≥ 100 ≥10 supporting reads
Sapoval-like [39]	≥20,000 mapped reads	VAF ≥ 2%, VAF < 50% DP ≥ 10 Mask extremes of genome + homoplasmic positions [68]
Tonkin-Hill-like [38]	Excessive number iSNVs (99.9th percentile) Outlier number of iSNVs with mid-VAFs, between 40% and 80%	VAF ≥ 5%, VAF < 50% DP ≥ 100 ≥5 supporting reads
CoVigator approach	≥50,000 mapped reads ≥29,000 bp horizontal coverage Excessive number iSNVs (99.9th percentile) Outlier number of iSNVs with mid-VAFs, between 40% and 80%	VAF ≥ 2%, VAF < 50% DP ≥ 100 ≥10 supporting reads Mask extremes of genome + homoplasmic positions [68] from indels ≤ 10 bp