Extension of MuPeXI to all Variant Callers

gistfile1.txt

--- a/MuPeXI.py
+++ b/MuPeXI.py
@@ -466,6 +466,7 @@ def create_vep_compatible_vcf(vcf_file, webserver, keep_tmp, outdir, file_prefix
 def extract_allele_frequency(vcf_sorted_file, webserver, variant_caller):
     print_ifnot_webserver('\tExtracting allele frequencies', webserver)
     allele_fractions = defaultdict(dict)
+    freq_colms=set(["AF","FREQ","FA"])

     if not variant_caller in ('MuTect','MuTect2'):
         allele_fractions = None # no variant caller detected
@@ -483,10 +484,18 @@ def extract_allele_frequency(vcf_sorted_file, webserver, variant_caller):
                 if not len(reference_allele) == len(altered_allele):
                     altered_allele = altered_allele[1:] if len(reference_allele) < len(altered_allele) else altered_allele
                     altered_allele = '-' if len(reference_allele) > len(altered_allele) else altered_allele
-                if variant_caller == 'MuTect':
-                    allele_fraction = columns[9].split(':')[format_fields.index('FA')].strip() # GT:AD:BQ:DP:FA
-                elif variant_caller == 'MuTect2':
-                    allele_fraction = columns[9].split(':')[format_fields.index('AF')].strip() # GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1
+                freq_col=freq_colms.intersection(format_fields)
+                if(len(freq_col)==0): #freebayes
+                    c9=columns[9].split(':')
+                    AO=c9[format_fields.index('AO')]
+                    if("," in AO):
+                        AO=AO.split(',')[0]
+                    AO=float(AO)
+                    DP=float(c9[format_fields.index('DP')]) #should use RO, but that is often zero near indels
+                    allele_fraction=str(AO/(AO+DP))
+                else:
+                    field_idx=format_fields.index(freq_col.pop())
+                    allele_fraction = columns[9].split(':')[field_idx].strip() # GT:AD:BQ:DP:FA
                 ID = '{chromosome}_{genomic_position}_{altered_allele}'.format(
                     chromosome = chromosome,
                     genomic_position = genomic_position if not altered_allele == '-' else int(genomic_position) + 1,