issue assigning variants occuring within an amplicon overlap region

[george-githinji]

Running to an issue with variant assignment of omicron datasets with the ARTIC pipeline reverts variants to the reference despite sufficient read support for the variants in the bam file.
The variants are occuring within amplicon overlap regions
Looking at the vcf report i see the following;

12:27:11] [artic-tools::check_vcf] variant at pos 23599: T->G
[12:27:11] [artic-tools::check_vcf] located within an amplicon overlap region
[12:27:11] [artic-tools::check_vcf] var pos does not match with that of previously identified overlap var, holding new var (and dropping held var at 23013)
[12:27:11] [artic-tools::check_vcf] variant at pos 23604: C->A
[12:27:11] [artic-tools::check_vcf] located within an amplicon overlap region
[12:27:11] [artic-tools::check_vcf] var pos does not match with that of previously identified overlap var, holding new var (and dropping held var at 23599)

Wondering if this is a known issue and how best to address this.

[hsnguyen]

This issue may introduce wrong ref. allele reversions. Because --strict option is useful to deal with some other bugs, I think it's best to mask these sites (assumed contamination) instead of pad them with ref alleles.

[george-githinji]

Thanks for the comment. Wondering which other bugs would be introduced by negating the --strict mode.

[hsnguyen]

Thanks for the comment. Wondering which other bugs would be introduced by negating the --strict mode.

I don't remember in details but somethings related to the conflicts between failed and passed vcf that makes bcftools failed.
Maybe this one, I think artic-tools::check_vcf somehow can help overcome the issue?