It could happen, we have duplicated samples in multiple VCF files. For that, we have a rule "compare" in the merge_vcfs snakemake file. However, that file assumes that the first listed file is the main one - hence leaves all the samples in this one and removes the duplicates from the rest of them. This list is however ordered alphabetically - but we should be able to tell python, which is the "main" file.
It could happen, we have duplicated samples in multiple VCF files. For that, we have a rule "compare" in the merge_vcfs snakemake file. However, that file assumes that the first listed file is the main one - hence leaves all the samples in this one and removes the duplicates from the rest of them. This list is however ordered alphabetically - but we should be able to tell python, which is the "main" file.