I think our current filtering approach filters out any heterozygous SNPs by default (if the bacterial SNP analysis workflow was adapted).
We should double check this again and also be transparent about this.
The downstream filter steps (like vcf-to-tab step) are only consistent if this is the case.
In addition, we need to check that the intermediate SNP output tables (in vcf_to_tab directory) make sense, not just for haploid organisms.
I will have some new tables generated shortly and will follow-up with this.
Just following up about this issue.
I think our current filtering approach filters out any heterozygous SNPs by default (if the bacterial SNP analysis workflow was adapted). We should double check this again and also be transparent about this.
The downstream filter steps (like vcf-to-tab step) are only consistent if this is the case.
In addition, we need to check that the intermediate SNP output tables (in vcf_to_tab directory) make sense, not just for haploid organisms.
I will have some new tables generated shortly and will follow-up with this.