Use low-confidence site filtering for AF trajectory analyses#28
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Ensures missing variants are distinguished from zero frequency values by applying depth and quality filters. Prevents low-confidence sites from biasing allele frequency analyses.
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Ensures missing variants are distinguished from zero frequency values by applying depth and quality filters, preventing low-confidence sites from biasing allele frequency analyses. This PR does not alter AF-weighted distance calculations.
Using
bcftools mpileup, all sites are initially filtered by base quality. Then, sites are filtered based on total AD. For allele frequency trajectory analyses, sites passing these filters are assigned an imputed AF=0 if the variant is absent in a given sample (representing AF=1 of the reference allele). Conversely, low-confidence sites that fail to meet these thresholds are assigned AF=`NA.Also adds minor changes to documentation.