Add DeepRVAT annotation pipeline #28
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…nnotations into a single file
add snakemake
Add snakemake, tensorflow and lock numpy
add nvidia channel
add python=3.8.17
Remove nvidia channel
Support strict
function more general
endast
commented
Oct 20, 2023
Marcel-Mueck
approved these changes
Oct 20, 2023
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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.