Question: annovar-build a ensembl db
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gravatar for walker
17 months ago by
walker20
walker20 wrote:

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!

database annovar • 558 views
ADD COMMENTlink modified 17 months ago by Kevin Blighe51k • written 17 months ago by walker20
0
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

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

ADD COMMENTlink written 17 months ago by Kevin Blighe51k
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