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validation (#889)
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v03_pipeline/lib/misc/validation.py

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@@ -155,7 +155,7 @@ def validate_sample_type(
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msg = f'Sample type validation error: dataset contains noncoding variants but is missing common coding variants for {reference_genome.value}. Please verify that the dataset contains coding variants.'
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raise SeqrValidationError(msg)
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if has_coding and not has_noncoding and sample_type != SampleType.WES:
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msg = 'Sample type validation error: dataset sample-type is specified as WGS but appears to be WES because it contains many common coding variants'
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msg = 'Sample type validation error: dataset sample-type is specified as WGS but appears to be WES because it contains many common coding variants but is missing common non-coding variants'
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raise SeqrValidationError(msg)
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if has_noncoding and has_coding and sample_type != SampleType.WGS:
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msg = 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants'

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