Added Support for all models needed for basic deeprvat run: AbSplice, CADD, SpliceAI, PrimateAI, DeepRIPE (hg2, k5 and parclip model) and DeepSEA. Performs PCA on DeepSEA annotations and merges the annotations into a single file. The pipeline uses BCF files created by the preprocessing steps as input, as well as a pvcf.txt file explaining the order of input files. The pipeline downloads and installs needed repositories, but some files have to be downloaded manually. See VEP Plugins page for instructions to download data needed for CADD, SpliceAI and PrimateAI Plugins.
What
Added Support for all models needed for basic deeprvat run: AbSplice, CADD, SpliceAI, PrimateAI, DeepRIPE (hg2, k5 and parclip model) and DeepSEA. Performs PCA on DeepSEA annotations and merges the annotations into a single file. The pipeline uses BCF files created by the preprocessing steps as input, as well as a pvcf.txt file explaining the order of input files. The pipeline downloads and installs needed repositories, but some files have to be downloaded manually. See VEP Plugins page for instructions to download data needed for CADD, SpliceAI and PrimateAI Plugins.