Genes missing in hg38 ref file

[sahilseth]

Hi I am using the recommended files and notices some genes important in our analysis are missing from the database:

For example:

library(dndscv)

env_dndscv = new.env()
env_dndscv

load("~/apps/dndscv_data/data/covariates_hg19_hg38_epigenome_pcawg.rda", envir = env_dndscv) 
refcds = "~/apps/dndscv_data/data/RefCDS_human_GRCh38_GencodeV18_recommended.rda"

ref_cds_genes = lapply(RefCDS, "[[", "gene_name") %>% unlist()
genes_miss = setdiff(env_dndscv$covs %>% rownames(), ref_cds_genes)
length(genes_miss)

2667

IGLL5 is one such example of a missing gene.