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05 01, 2019;8 (5):

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.

Kristian Hanghøj, Ida Moltke, Philip Alstrup Andersen, Andrea Manica, Thorfinn Sand Korneliussen
Author Information
  1. Kristian Hanghøj: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark.
  2. Ida Moltke: Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
  3. Philip Alstrup Andersen: Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
  4. Andrea Manica: Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
  5. Thorfinn Sand Korneliussen: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark.
PMID: 31042285 DOI: 10.1093/gigascience/giz034

Abstract

BACKGROUND: The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data.
RESULTS: We introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process.
CONCLUSION: The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).

Keywords

Jacquard coefficients genotype likelihood high-throughput sequencing data inbreeding next-generation sequencing population genetics relatedness estimation threading

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MeSH Term

Genetics, Population
Genotype
Genotyping Techniques
High-Throughput Nucleotide Sequencing
Humans
Inbreeding
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Software
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 13

Word Cloud

Created with Highcharts 10.0.0datarelatednessprogramestimationsequencingindividualshigh-throughputinbredHTSgenotypeJacquardcoefficientsinbreedingBACKGROUND:pairspossiblypreviouslypossiblesamplesobtainreliablecallscaselow-coverageRESULTS:introducengsRelateV2majorrevisionngsRelateV1originallyallowedamongnon-inbrednewrevisedversiontakesaccountpossibilityestimating9condensedalongvariousstatisticsthreadedscaleslinearlynumbercoresallocatedprocessCONCLUSION:availableopensourceC/C++GPLlicensehostedhttps://githubcom/ANGSD/ngsRelatefacilitateeasyanalysisableworkdirectlycommonlyusedcontainerformatsrawsequenceBAM/CRAMsummaryVCF/BCFFastaccuratepresencelikelihoodnext-generationpopulationgeneticsthreading

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