Add allele frequency filter

Author: BioWilko

artic/vcf_filter.py

@@ -22,13 +22,19 @@ def __init__(self, no_frameshifts, min_depth):
         self.min_depth = min_depth
         self.min_variant_quality = 10
         self.min_frameshift_quality = 30
+        self.min_allele_frequency = 0.6
 
     def check_filter(self, v):
         qual = v.QUAL
 
         if qual < self.min_variant_quality:
             return False
 
+        # Filter out low allele frequency variants
+        allele_freq = v.INFO.get("AF")
+        if allele_freq and allele_freq < self.min_allele_frequency:
+            return False
+
         if not in_frame(v):
             if self.no_frameshifts:
                 return False