Merge pull request #51 from jodyphelan/dev

bugfix
jodyphelan · Aug 30, 2024 · 3b4c6e2 · 3b4c6e2
2 parents 67cd363 + 96779c4
commit 3b4c6e2
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/scripts/combine_vcf_variants.py b/scripts/combine_vcf_variants.py
@@ -173,11 +173,13 @@ def has_md_tag(bam):
             hap = ''.join(alts)
             if 'DP4' in v.info:
                 haplotypes_by_strand[hap] = int(v.info['DP4'][2])+int(v.info['DP4'][3])
+            elif 'SAF' in v.info:
+                haplotypes_by_strand[hap] = int(v.info['SAF'][0])
+                haplotypes_by_strand[hap.lower()] = int(v.info['SAR'][0])
             elif 'AD' in v.samples[0]:
                 haplotypes_by_strand[hap] = int(v.samples[0]['AD'][1])
 
 
-
     haplotypes = Counter()
     for h,count in haplotypes_by_strand.items():
         haplotypes[h.upper()] += count