--- a/pileup_to_vcf.py	Mon Feb 18 11:32:50 2013 -0500
+++ b/pileup_to_vcf.py	Mon Feb 18 19:11:47 2013 -0600
@@ -49,7 +49,7 @@
   parser.add_option( '-i', '--input', dest='input', help='The input pileup file (else read from stdin)' )
   parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
   # filters
-  parser.add_option( '-c', '--min_coverage', type='int', default='0', dest='min_coverage', help='The minimum read coverage depth to report a variant [default 0]' )
+  parser.add_option( '-c', '--min_coverage', type='int', default='1', dest='min_coverage', help='The minimum read coverage depth to report a variant [default 1]' )
   parser.add_option( '-r', '--report_depth', type='choice', choices=['all','ref','qual'], default='ref', dest='report_depth', help='Coverage depth as: ref - reads covercovering base, all - reads spanning base, qual - reads with base call above min_base_quality' )
   parser.add_option( '-b', '--min_base_quality', type='int', default='0', dest='min_base_quality', help='The minimum base quality for a base call to be counted' )
   parser.add_option( '-f', '--min_allele_freq', type='float', default='.5', dest='min_allele_freq', help='The minimum frequency of an allele for it to be reported (default .5)' )
@@ -194,6 +194,8 @@
               deletions[indel] += 1
             else:
               deletions[indel] = 1
+        elif base == '*' : # a deletion from a prior base
+          qi += 1
         elif base == '^' : #start of read (followed by read quality char)
           read_mapping_qual = ord(bases[bi]) - 33 
           bi += 1
@@ -201,6 +203,8 @@
           pass # no associated quality in either bases or quals
       dp = rdp if dp_as == 'ref' else qdp if dp_as == 'qual' else adp
       if debug: print >> sys.stderr, "snps: %s\tins: %s\tdel: %s" % (snps,insertions,deletions)
+      if dp < max(1,min_coverage) :
+        continue
       # output any variants that meet the depth coverage requirement
       vcf_pos = pos
       vcf_ref = ref