{"repo":"zhanxw/seqminer","free":true,"listed":false,"github":"https://github.com/zhanxw/seqminer","clone":"git clone https://github.com/zhanxw/seqminer.git","description":"Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R","language":"C","stars":33,"topics":["sequencing","annotation","next-generation-sequencing","meta-analysis","vcf","bcf","tabix","bgen","plink","workflow"],"license":null,"category":"workflow-automation","readme_excerpt":"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 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., ","default_branch":null,"files":null,"tree":[],"storefront":"/r/zhanxw","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/zhanxw/seqminer/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}