proxy_match: Extract SNPs from vcf file
In MRCIEU/gwasvcf: Tools for Dealing with GWAS Summary Data in VCF Format

proxy_match

R Documentation

Extract SNPs from vcf file

Description

Finds proxies if necessary

Usage

proxy_match(
  vcf,
  rsid,
  bfile = NULL,
  proxies = "yes",
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1,
  rsidx = NULL,
  dbfile = NULL
)

Arguments

`vcf`	vcf file name
`rsid`	list of rs IDs
`bfile`	ld reference panel (plink)
`proxies`	="yes" If SNPs are absent then look for proxies (yes) or not (no). Can also mask all target SNPs and only return proxies (only), for testing purposes
`tag_kb`	=5000 Proxy parameter
`tag_nsnp`	=5000 Proxy parameter
`tag_r2`	=0.6 Proxy parameter
`threads`	Number of threads to use (=1)
`rsidx`	Path to rsidx index
`dbfile`	ld tag database (sqlite)