variant discrepancy between in ivar and snpeff annotated file

[wantingwei]

Description of the bug

I am recently running the viralrecon 2.6.0 on some sars-cov-2 sequences; I noticed that ivar.tsv output doesn't match with the snpeff. annotated vcf as well as the variant long table when there is polymorphism. I have attached the output. also to visualize things easier
Here is the snpeff vcf file, there is only one mutation at position 23606

When looking at the tsv file, there is two variants at the same mutation.

I try to add the command in the config file but doesn't fix the issue. withName: 'IVAR_VARIANTS_TO_VCF' {
ext.args = params.protocol == 'amplicon' ? '--ignore_strand_bias --ignore_merge_codons' : '--ignore_merge_codons'
}
I would appreciate if people can take a look and help me solve it. Thank you!

Command used and terminal output

No response

Relevant files

stock-variant.zip

System information

No response

[wantingwei]

I am wondering if it would be possible for the issue to be raised due to lines 449 -451 in the script. https://github.com/nf-core/viralrecon/blob/master/bin/ivar_variants_to_vcf.py

[saramonzon]

Hi @wantingwei ! This issue is related to #337

As we talked in private, we are working on an updated version of ivar_variants_to_vcf script which will fix the issue.
We'll try to share it asap :)