False positive argmatch results about drprg HOT 1 CLOSED

Suggest you turn a catalogue into three catalogues

Part A: nucleotide matches
Use VCF definition of catalogue, and match Drprg vcf with catalogue vcf. Some trickiness with indel normalisation.

Part B: amino variants
First translate the pandora-inferred sequence into amino sequence
Then,

• catalogue has two dictionaries. Both have key which is amino position /index in the reference amino sequence. First dictionary has value which is array of amino acids which cause resistance. Second dictionary has value which is array of amino acids which definitely don't cause resistance. WHO and others starting to provide these "definitely not a resistance variant" lists, could be useful to report.

Finally notice if there is

• stop codon
• Part of the Pandora sequence has zero coverage, signifying truncated gene

Part C

• rule about whether frameshifts or stop codon or truncations in a gene are meant to cause resistance. Frameshift detection by aligning amino sequence seems most reliable as you incorporate all variants at the same time. Otherwise you have multiple nucleotide positions nearby affecting the same codon

from drprg.