Retain qual scores for dragen/dragen cnv standardization

Author: kjaisingh

src/sv-pipeline/05_annotation/scripts/add_gq_to_vcf.py

@@ -0,0 +1,33 @@
+import gzip
+import sys
+
+# Input and output files
+in_vcf = "/Users/kjaising/Downloads/cluster_batch.dragen.fmt.vcf.gz"
+out_vcf = "/Users/kjaising/Downloads/cluster_batch.dragen.gq.fmt.vcf.gz"
+
+# Default GQ value to use
+DEFAULT_GQ = "999"
+
+with gzip.open(in_vcf, 'rt') as f_in, gzip.open(out_vcf, 'wt') as f_out:
+    for line in f_in:
+        if line.startswith('#'):
+            if line.startswith('#CHROM'):
+                f_out.write('##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n')
+            f_out.write(line)
+        else:
+            fields = line.strip().split('\t')
+            format_idx = 8
+            format_fields = fields[format_idx].split(':')
+            
+            if 'GQ' not in format_fields:
+                format_fields.insert(1, 'GQ')
+                fields[format_idx] = ':'.join(format_fields)
+                
+                for i in range(9, len(fields)):
+                    sample_values = fields[i].split(':')
+                    sample_values.insert(1, DEFAULT_GQ)
+                    fields[i] = ':'.join(sample_values)
+            
+            f_out.write('\t'.join(fields) + '\n')
+
+print(f"Created new VCF with GQ fields at: {out_vcf}")

src/svtk/svtk/standardize/std_dragen.py

@@ -146,6 +146,9 @@ def standardize_info(self, std_rec, raw_rec):
         # Define ALGORITHMS
         std_rec.info['ALGORITHMS'] = ['dragen']
 
+        # Retain QUAL score
+        std_rec.qual = raw_rec.qual
+
         return std_rec
 
     def standardize_alts(self, std_rec, raw_rec):

src/svtk/svtk/standardize/std_dragen_cnv.py

@@ -69,6 +69,9 @@ def standardize_info(self, std_rec, raw_rec):
         # Define ALGORITHMS
         std_rec.info['ALGORITHMS'] = ['depth']
 
+        # Retain QUAL score
+        std_rec.qual = raw_rec.qual
+
         return std_rec
 
     def standardize_alts(self, std_rec, raw_rec):