Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read 'RareMETAL' summary statistics files; (3) read tables from a 'tabix'-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

SEQMINER2

Table of Contents

• Introduction
• Download
• Showcase
  • Index VCF/BCF files
  • Query VCF/BCF files
  • Query BGEN/PLINK files
  • Command line linterface

Introduction

Seqminer is a highly efficient R-package for retrieving sequence variants from biobank scale datasets of millions of individuals and billions of genetic variants. It supports all variant types, including multi-allelic variants and imputation dosages. It takes VCF/BCF/BGEN/PLINK format as input file, indexes, queries them based upon variant-based index and loads them as R data types such as list or matrix.

Download

Install the development version (devtools package is required):

devtools::install_github("zhanxw/seqminer")

Showcase

Here are some examples of how to use seqminer to index and query files in real-life scenarios.

Index VCF/BCF files

library(seqminer)
bcf.ref.file <- "input.bcf"
bcf.idx.file <- "input.bcf.scIdx"
out <- seqminer::createSingleChromosomeBCFIndex(bcf.ref.file, bcf.idx.file)

or

vcf.ref.file <- "input.vcf.gz"
vcf.idx.file <- "input.vcf.gz.scIdx"
out <- seqminer::createSingleChromosomeVCFIndex(vcf.ref.file, vcf.idx.file)

This would generate variant-based index that works with commonly used sequence variant file format, such as VCF/BCF files.

Query VCF/BCF files

Query VCF file:

vcf.ref.file <-  "input.vcf.gz"
vcf.idx.file <-  "input.vcf.gz.scIdx"
tabix.range <- "1:123-1234"
geno <- seqminer::readSingleChromosomeVCFToMatrixByRange(vcf.ref.file, tabix.range, vcf.idx.file)

Query BCF file:

bcf.ref.file <- "input.bcf"
bcf.idx.file <- "input.bcf.scIdx"
tabix.range <- "1:123-1234"
geno <- seqminer::readSingleChromosomeBCFToMatrixByRange(bcf.ref.file, tabix.range, bcf.idx.file)

Querying multiple regions is also doable, simply specify multiple regions and separte them by a comma, e.g. "1:123-124,1:1234-1235".

Output example (column represents variants, row represents individuals):

Query BGEN/PLINK files

Query BGEN file:

bg.ref.file <- "input.bgen"
bg.range <- "1:123-1234"
geno.mat <- seqminer::readBGENToMatrixByRange(bg.ref.file, bg.range)
geno.list <- seqminer::readBGENToListByRange(bg.ref.file, bg.range)

Make sure that bgen file has an index file *.bgi in the same folder.

Query PLINK file:

plink.ref.file <- "input"
geno <- seqminer::readPlinkToMatrixByIndex(plink.ref.file, sampleIndex=1:20000, markerIndex=1:100)

Command line linterface

We also developed a seqminer command line interface:

./queryVCFIndex.intel input.vcf.gz input.vcf.gz.scIdx 1:123-1234

Citation:

Yang, L., Jiang, S., Jiang, B., Liu, D. J., & Zhan, X. (2020). Seqminer2: An Efficient Tool to Query and Retrieve Genotypes for Statistical Genetics Analyses from Biobank Scale Sequence Dataset. Bioinformatics

Zhan, X. and Liu, D. J. (2015), SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations. Genet. Epidemiol., 39: 619–623. doi:10.1002/gepi.21918