Hi, I download the latest ensembl hg38 fa and gtf myself, and it occurrs me how to build my annovar db based on these two file. Also, what's the difference between the different --format in annovar ? Please help!
Just use the in built ANNOVAR functions for annotation with ensembl: Switching to hg38 Ensembl gene annotation.
The --format parameter has different meanings in different ANNOVAR functions. If can just execute the functions without any command-line parameters in order to see the options available. For example, for convert2annovar.pl, format relates to the input file format, such as VCF 'old', VCF v4, etc. For other commands, it may relate to the annotation source, e.g., --format refGene or --format ensGene
Kevin
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