Table of Contents
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):
devtools::install_github("zhanxw/seqminer")
Here are some examples of how to use seqminer to index and query files in real-life scenarios.
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 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 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)
We also developed a seqminer command line interface:
./queryVCFIndex.intel input.vcf.gz input.vcf.gz.scIdx 1:123-1234
Citation: