stack1kg {ldblock}R Documentation

couple together a group of VCFs

Description

couple together a group of VCFs

Usage

stack1kg(chrs = as.character(1:22), index = FALSE, useEBI = TRUE)

Arguments

chrs

a vector of chromosome names for extraction from 1000 genomes VCF collection

index

logical telling whether VcfStack should attempt to create the local index; for 1000 genomes, the tbi are in the cloud and will be used by readVcf so FALSE is appropriate

useEBI

logical(1) defaults to TRUE ... use tabix-indexed vcf from EBI

Value

VcfStack instance

Note

The seqinfo component of returned stack will have NA for genome. Please set it manually; for useEBI=TRUE this would be GRCh38.

Examples

if (interactive()) {
  st1 = stack1kg()
  st1
  }

[Package ldblock version 1.18.0 Index]