Mapping and annotation using the T2T-CHM13 reference genome

Question

[greekkey]

Hi, I am planning to analyzing human WGS data with the T2T-CHM13 genome as reference, which is now regarded as the complete sequence of a human genome. I am wondering where I can get the resources for performing BQSR, VQSR and annotation (I use aNNOVAR). I appreciate for any comments and suggestions.

[Ranold Grijon]

HI, did you able to annotate your vcf file? I am planning to annotate my vcf file using annovar. How did you specify buildver in annovar for T2T-chm13? Is it --buildver T2T-CHM13? How did you make the databases for chm13?