I want to use the BaseRecalibrator function and have the following question:
I aligned my WGS to the GRCh38.p13. The problem is, that even after looking for hours I still can not find the db SNP VCF which uses the GRCh38.p13. The latest version of the db SNP VCF version that I could find uses GRCh38.p12 (https://ftp.ncbi.nih.gov/snp/latest_release/VCF/).
My question now is, if that might cause any problems if i use the "outdated" VCF file for my alignment, which was mapped to GRCh38.p13.
If somebody could point me to a db SNP VCF file which uses the GRCh38.p13 assembly, that would be even better!
Thank you very much!
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