getGnomADvariants: Get gnomAD VCF file using tabix.

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Get gnomAD VCF file using tabix.

Description

Function retrieves variant data from gnomAD VCF files using tabix for a specified set of genomic regions. It allows users to select the gnomAD version and server location (Google, Amazon, or Microsoft) for fetching the data.

Usage

getGnomADvariants(
  chr.names,
  starts,
  ends,
  INFO.filter = NULL,
  version = "3.1.2",
  server = "random"
)

Arguments

chr.names	Chromosome names.
starts	Start positions.
ends	End positions.
INFO.filter	Parse only filtered INFO ID. Default is to parse all IDs.
version	The gnomAD version. Default to latest version 3.1.2.
server	Server locations: "google", "amazon", or "microsoft". Default is random.

Value

A data.table of VCF.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.