Towards pan-genome read alignment to improve variation calling

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BMC Genomics. 2018 May 09;19(Suppl 2):87

Title: Towards pan-genome read alignment to improve variation calling
Author: Valenzuela, Daniel; Norri, Tuukka; Välimäki, Niko; Pitkänen, Esa; Mäkinen, Veli
Publisher: BioMed Central
Date: 2018-05-09
Abstract: Abstract Background Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation. Results We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation – a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: . Conclusions Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.
Subject: Pan-genome reference
Variation calling
Read alignment

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