Functional-GS
Dunia Pino del Carpio, Roberto Lozano, et al. Channel created to compile and share code for a functional GS article. We aim to improve genomic prediction models by
-prioritizing SNPs with known biological/genomic function and following a multikernel approach
-adjusting kinship matrices with an LD weight/score correction
-annotating snps into genome structure categories: intro,exon,UTRs,etc
-including heritability values for genome structure categories
Scripts short description:
getgformat.sh <- wrapper to transform a GBS vcf filtered file to the oxford "g" format required for running IMPUTE2
Folds.R<-R script to subset a large list of clone names to assign them into folds for "crossvalidation" GWAS
bio_kernels.R<-R script to subset a large list of SNP names into lists based on their biological annotation, these SNP subsets will then be used for contruction Genomic relationship matrices (GRMs)