Currently optional fields like GL and GP are still included in the output VCF when they are not in use and just have the null value of ".". This slightly increases VCF size and may require some minor work around in downstream analysis. It also may cause confusion as to why these fields are empty. In short it would be best to omit them completely if they aren't used.
timothymillar
commented
3 years ago
Currently optional fields like GL and GP are still included in the output VCF when they are not in use and just have the null value of
".". This slightly increases VCF size and may require some minor work around in downstream analysis. It also may cause confusion as to why these fields are empty. In short it would be best to omit them completely if they aren't used.