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andersen-lab / ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
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weird variant TSV output #179

Open Norina28 opened 2 months ago

Norina28 commented 2 months ago

Describe the bug Hello, I have a weird variant TSV output when I provide the gff file with a reference with multiple contigs. More or less each variant is duplicate/triplicate with the same values except the annotation columns( GFF_FEATURE, REF_CODON, REF_AA, ALT_CODON, ALT_AA). And when I go to search the GFF features, they belong to other contigs, the only thing it matches is the nt number. For example pos 30 of contig1, I get the gff features of pos 30 of other contigs.

To Reproduce this is the command I ran: samtools mpileup -aa -A -d 0 -B -Q 0 --reference MRSN599975.fasta MRSN599975negative_sort.bam | ivar variants -p MRSN599975negative -r MRSN599975.fasta -g annot.gff

Expected behavior If I ran the variant without gff file everything is fine.

Screenshots

Screenshot 2024-05-02 at 12 32 55 PM

Thank you!

Norina28 commented 1 month ago

Does anyone have any idea why it is happening?