Identification of non-synonymous Variants

[nitinShukla1912]

As Authors have mentioned that for identification of non-synonymous variants they have used ivar,
So I belive they might have used (samtools | ivar) for the identification of non synonymous variants for species of interest.
But somehow I am unable to generate output file with Amino Acid mutation, I did validated gff3 file using https://genometools.org/cgi-bin/gff3validator.cgi

How this issue can be resolved?

Also which bam file to consider from tmp file (virus_pathogen_database.mmi.*_input.fastq.sort.bam), and If i want to identify for specific species then the output which is generated for all the species that mapped against the reference database, is there a way to get the output for respective species only.

[mtisza1]

Hi,

First, I want to apologize for not answering this issue until now. I did not have the correct settings on this repo, and I wasn't getting the notifications for new issues.

For your question, you probably want to make and issue on the ivar github.

But I may be able to help a bit:

I used reads specific to my reference of interested extracted from accessions_final_threshold1.bam files in the EsViritu temp files.

Are you specifying your .gff file with the -g flag when you use the ivar variants command?