Remove CHR2 and END2 from INS in CleanVcf (#631)

broadinstitute · May 2, 2024 · d3514d4 · d3514d4
1 parent e0069ff
commit d3514d4
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/src/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py b/src/sv-pipeline/scripts/format_svtk_vcf_for_gatk.py
@@ -137,7 +137,7 @@ def is_null(val):
     is_ddup = svtype == 'CPX' and 'dDUP' in record.info.get('CPX_TYPE', '')
     if svtype == 'BND' or svtype == 'INS' or svtype == 'CTX' or is_ddup:
         record.stop = record.start + 1
-    if svtype == 'CPX':
+    if svtype == 'CPX' or svtype == 'INS':
         if 'CHR2' in record.info:
             record.info.pop('CHR2')
         if 'END2' in record.info:

diff --git a/src/svtk/svtk/svfile.py b/src/svtk/svtk/svfile.py
@@ -107,7 +107,10 @@ def __init__(self, record):
 
         chrA = record.chrom
         posA = record.pos
-        chrB = record.info['CHR2']
+        if 'CHR2' in record.info:
+            chrB = record.info['CHR2']
+        else:
+            chrB = chrA
         posB = record.stop
         name = record.id