Code and data for analyzing SNP annotation agreement across ANNOVAR, SnpEff, and VEP using Ensembl and RefSeq gene models. Includes reproducible scripts for genome-wide analysis, a colorectal cancer case study, and assessment of downstream pathway interpretation.
In the Scripts Directory and update the path information.
For the ensembl_nested_UniProt.py Line 423 - update your HGNC Mapping CSV file path Line 479 - update the file path for the HRC data folder or directory Line 480 - put where you would like the summary CSV to be outputed