Hi All,
I am interested in generating technical annotations from various VCF files created by different variant callers e.g. medaka, clair3 etc. As standard technical annotations such as DP, AF, AC, are either not included by default in certain tools (medaka) and I want to make sure that they are calculated in a standardised way for all VCFs, I am using VAFATOR to obtain technical annotations.
However, there are a few issues with this tool and some errors thrown by the program are rather obscure and cannot be resolved (I have already raised this on the dev github page!)
I am just wondering if there are any other tools that can be used to obtain technical annotations for microbial long-read VCF files.
Any help/pointers/suggestions would be greatly appreciated! :)
