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Plant Genome. 2018 Jul;11(2). doi: 10.3835/plantgenome2018.01.0006.

QTLseqr: An R Package for Bulk Segregant Analysis with Next-Generation Sequencing.

Abstract

Next-Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G'. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G' values, and log (-values), enabling identification and plotting of QTL. The source code is available at .

PMID:
30025013
DOI:
10.3835/plantgenome2018.01.0006
[Indexed for MEDLINE]
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