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hassansaei / VNtyper

A tool to genotype MUC1 coding VNTR in ADTKD
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Red_Zone in Kestrel_concat not defined #2

Closed berntpopp closed 1 month ago

berntpopp commented 3 months ago

The value "Red_Zone" in th confidence column of the Kestrel_concat dataframe is never assigned or defined and only used once. What does this do?

 Kestrel_concat = Kestrel_concat[Kestrel_concat['Confidence'] != 'Red_Zone']
hassansaei commented 2 months ago

The value "Red_Zone" in th confidence column of the Kestrel_concat dataframe is never assigned or defined and only used once. What does this do?

 Kestrel_concat = Kestrel_concat[Kestrel_concat['Confidence'] != 'Red_Zone']

The red zone refers to variants that have been identified with a depth score (DS) below the threshold and are subsequently filtered out. In the upcoming version, which is currently in preparation, this annotation will be excluded from the script.