SMAP: a versatile approach to read-backed haplotyping in stacked NGS read data

Tom Ruttink, Elisabeth Veeckman, Dries Schaumont, Sabine Van Glabeke, Annelies Haegeman, Hilde Muylle, Isabel Roldán-Ruiz, Jean-Paul Sampoux, Philippe Barre, Stephen Byrne, Jie Kang, Felix Van der Jeugt , Peter Dawyndt

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We have developed a computational algorithm called "SMAP" (short for Stack Mapping Anchor Points) for read-backed haplotyping in “stacked” NGS reads, applicable to highly multiplex amplicon sequencing (HiPlex) or Genotyping-by-Sequencing (GBS) data. In highly heterozygous species, up to one-third of the loci may display polymorphic read alignments. In addition, SNPs shared between multiple alleles confound analysis of allele frequency shifts. The SMAP algorithm improves allele frequency estimation in pool-Seq data or discrete genotype calls in individuals and groups neighboring SNPs into multi-allelic haplotype markers per locus, thus increasing genetic resolution.
Oorspronkelijke taalNederlands
PublicatiestatusGepubliceerd - 15-jan-2020

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