diff --git a/AnnotatorCore.py b/AnnotatorCore.py index 4fe038f..8db447d 100644 --- a/AnnotatorCore.py +++ b/AnnotatorCore.py @@ -196,9 +196,9 @@ def setsampleidsfileterfile(f): GC_VAR_ALLELE_1_HEADER, GC_VAR_ALLELE_2_HEADER] # columns for structural variant annotation -SV_GENEA_HEADER = ['SITE1_GENE', 'GENEA', 'GENE1'] -SV_GENEB_HEADER = ['SITE2_GENE', 'GENEB', 'GENE2'] -SV_TYPE_HEADER = ['SV_CLASS_NAME', 'SV_TYPE'] +SV_GENEA_HEADER = ['SITE1_GENE', 'GENEA', 'GENE1', 'SITE1_HUGO_SYMBOL'] +SV_GENEB_HEADER = ['SITE2_GENE', 'GENEB', 'GENE2', 'SITE2_HUGO_SYMBOL'] +SV_TYPE_HEADER = ['SV_CLASS_NAME', 'SV_TYPE', 'CLASS'] SV_TYPES = ['DELETION', 'TRANSLOCATION', 'DUPLICATION', 'INSERTION', 'INVERSION', 'FUSION', 'UNKNOWN'] UNKNOWN = 'UNKNOWN'