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Validation Update: Add a warning for GERMLINE variants in MAF and SV files #63

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merged 1 commit into from
Oct 21, 2024
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Validation Update: Add a warning for GERMLINE variants in MAF and SV files #63

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7 changes: 7 additions & 0 deletions scripts/importer/validateData.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2397,6 +2397,9 @@ def checkMutationStatus(self, value):
if value.lower() not in ['none', 'germline', 'somatic', 'loh', 'post-transcriptional modification', 'unknown', 'wildtype'] and value != '':
self.logger.warning('Mutation_Status value is not in MAF format',
extra={'line_number': self.line_number, 'cause': value})
if value.lower() == 'germline':
self.logger.warning('GERMLINE variant identified from the Mutation_Status value. If this variant is not meant for public release, please remove it.',
extra={'line_number': self.line_number, 'cause': value})
return True

class ClinicalValidator(Validator):
Expand Down Expand Up @@ -3216,6 +3219,10 @@ def checkSVstatus(sv_status):
if sv_status is None:
self.logger.warning('No value in SV_Status, assuming the variant is SOMATIC',
extra={'line_number': self.line_number})
elif sv_status.lower() == 'germline':
self.logger.warning('GERMLINE variant identified from the SV_Status value. If this variant is not meant for public release, please remove it.',
extra={'line_number': self.line_number,
'cause': sv_status})
else:
if not sv_status.lower() in ['somatic', 'germline']:
self.logger.error('Invalid SV_Status value: possible values are [SOMATIC, GERMLINE]',
Expand Down
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