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NorwegianVeterinaryInstitute / DPI

Differences between Pairs of Isolates
BSD 3-Clause "New" or "Revised" License
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External bug - investigate impact ? #31

Open evezeyl opened 6 days ago

evezeyl commented 6 days ago

nucdiff formating of vcf variant files that are then "prepared" aka, fix the format, before annotation with vcf-annotator has "bugs" This is fixed with prep_vcf_annotator.py

  1. Adding info Column
  2. To investigate : in some case N is writen in REF and its NaN in ALT - This makes vcf-annotator bug. I fixed this by replacing NaN by "." But this might not bee good For eventual analysis of annotated snps, - REF with N must be then filtered out This also means that some differences might not be true ... errror - we need to find a way to validate
evezeyl commented 4 days ago

commit fix: ddc9ded6f2d267131681cb8aec62b52654016acf