Issue with ivar variants Output in Galaxy: Missing Annotations

1

Dear Galaxy Support Team,

I am analyzing genetic changes between passages 1 and 10 of Avian Paramyxovirus 1 (Newcastle Disease Virus), using the reference Lasota virus. I followed these steps:

  1. Generated a BAM output file using samtools mpileup in the terminal.
  2. Uploaded the BAM file to Galaxy and used it with ivar variants.

While the tool ran successfully, the output file for both P1 and P10 contains “NA” values for several annotation fields, specifically:

  • REF_CODON
  • REF_AA (Reference Amino Acid)
  • ALT_CODON (Altered Codon)
  • ALT_AA (Altered Amino Acid)

Here is an example of the output:
REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA POS_AA
AF077761.1 95 A T 1 0 74 509 72 45 0.996086 511 0 TRUE NA NA NA NA NA NA
AF077761.1 99 A G 5 2 59 516 79 46 0.990403 521 0 TRUE NA NA NA NA NA NA
AF077761.1 130 C T 2 0 55 616 112 47 0.996764 618 0 TRUE NA NA NA NA NA NA
AF077761.1 139 T C 2 0 55 645 108 47 0.996909 647 0 TRUE NA NA NA NA NA NA
AF077761.1 142 G A 4 1 55 625 105 46 0.993641 629 0 TRUE NA NA NA NA NA NA
AF077761.1 148 A G 1 0 62 658 130 48 0.998483 659 0 TRUE NA NA NA NA NA NA

I understand that “NA” means “Not Available” or “Not Applicable,” but I need these annotations for my analysis. Can you please help me understand why these fields are showing “NA” and how I can obtain the missing annotations?

Thank you

Regards,
Deepa Chaudhary

2

Hi @Deepa

You will need to provide a reference annotation to produce these fields.

This is the last input on the form:

Coordinates of ORFs for optional variant effect prediction - optional

Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level. (-g)

Hope this helps! :slight_smile: