# THRESHOLDS FOR MISANNOTATED GENES

# remove genes overlapping more than this percent of gene body with a single TE
threshGeneBodyOverlapSingleTE <- 0.7

# remove genes overlapping more than this percent of gene body in total with multiple TEs
threshGeneBodyOverlapMultipleTE <- 0.9

# segments must have greater than this amount of coverage for all species
threshMinCoverageAcrossSpecies <- 0.8

# genes must overlap with at least this percent of their gene body with high coverage segments
threshGeneBodyOverlapHighCovSegments <- 0.9

# remove genes whose gene body overlap more than this percent with complex SV regions
threshGeneBodyOverlapComplexRegion <- 0.7