bindcadd_snv: bind CADD scores of Kircher et al. 2014 to a GRanges instance
In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description Usage Arguments Details Value Note Author(s) References Examples

bind CADD scores of Kircher et al. 2014 to a GRanges instance; by default will use HTTP access at UW

bindcadd_snv(
  gr,
  fn = "http://krishna.gs.washington.edu/download/CADD/v1.0/1000G.tsv.gz"
)

`gr`	query ranges to which CADD scores should be bound
`fn`	path to Tabix-indexed bgzipped TSV of CADD as distributed at krishna.gs.washington.edu on 1 April 2014

joins CADD fields at addresses that match query; the CADD fields for query ranges that are not matched are set to NA

GRanges instance with additional fields as obtained in the CADD resource

This software developed in part with support from Genentech, Inc.

VJ Carey <stvjc@channing.harvard.edu>

M Kircher, DM Witten, P Jain, BJ O'Roak, GM Cooper, J Shendure, A general framework for estimating the relative pathogenicity of human genetic variants, Nature Genetics Feb 2014, PMID 24487276

 ## Not run: 
  data(ebicat_2020_04_30)
  g2 = as(ebicat_2020_04_30, "GRanges")
 # would need to lift over here 
  bindcadd_snv( g2[which(seqnames(g2)=="chr2")][1:20] )
  
## End(Not run)