feat: exclude sequences with many mixed sites
@@ -58,6 +58,7 @@ if __name__ == '__main__':
to_exclude |= snp_clusters>args.snp_clusters
to_exclude |= rare_mutations>args.rare_mutations
to_exclude |= np.abs(clock_deviation+rare_mutations)>args.clock_plus_rare
+ to_exclude |= metadata.QC_mixed_sites=='bad'
# write out file with sequences flagged for exclusion
with open(args.output_exclusion_list, 'w') as excl:
