Hello,
I’m interested in using the nextclade output to detect the presence of specific amino acids associated with ab resistance in the F gene of RSV. Some of the amino acids I’m trying to confirm the presence of are in the reference genome used in the nextclade dataset, so I’m looking at the cds translation output to be able to confirm there is a specific amino acid at a specific position. (ex. Q at amino acid position 209 )
I see in the documentation that insertions won’t be included in the cds translation.
https://docs.nextstrain.org/projects/nextclade/en/stable/user/output-files/03-translations.html
Are any considerations/limitations of parsing the cds translation output, in terms of handing indels / frameshifts? Would it be a better approach to change the reference to one that doesn’t have my resistance mutation of interest?
Thanks in advancce!