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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.


Install the development version (devtools package is required):



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

Index VCF/BCF files

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


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".

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)

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:

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


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