For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION to output such a VCF. However to get INFO such as AC and MQ I need to follow up with GenotypeGVFs, and there doesn't seem to be an option to keep all positions when using this. In the end I must have a VCF which contains all possible variants and any position with zero coverage. Is there a way to generate a VCF with every reference position that includes AC and MQ values.
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