title: BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.
abstract: Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen by chance but are likely to denote autozygosity, whereby both copies of the genome descend from the same recent ancestor. Early tools to detect RoH used genotype array data, but substantially more information is available from sequencing data. Here, we present and evaluate BCFtools/RoH, an extension to the BCFtools software package, that detects regions of autozygosity in sequencing data, in particular exome data, using a hidden Markov model. By applying it to simulated data and real data from the 1000 Genomes Project we estimate its accuracy and show that it has higher sensitivity and specificity than existing methods under a range of sequencing error rates and levels of autozygosity.
  
  
  
  BCFtools/RoH and its associated binary/source files are freely available from https://github.com/samtools/BCFtools
  
  
  
  vn2@sanger.ac.uk or pd3@sanger.ac.uk
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton and.
authors.forename: Vagheesh
authors.initials: V
authors.lastname: Narasimhan
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton and.
authors.forename: Petr
authors.initials: P
authors.lastname: Danecek
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK.
authors.forename: Aylwyn
authors.initials: A
authors.lastname: Scally
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton and.
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton and.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton and.
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
mesh_terms: D059472:Exome; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D012984:Software
references.citation: Nature. 2012 Nov 1;491(7422):56-65
references.pmid: 23128226
references.citation: Bioinformatics. 2014 Oct 15;30(20):2852-9
references.pmid: 24966365
references.citation: Am J Hum Genet. 2010 Apr 9;86(4):526-39
references.pmid: 20303063
references.citation: BMC Genomics. 2011 Sep 23;12:460
references.pmid: 21943305
references.citation: Genome Res. 2009 Feb;19(2):318-26
references.pmid: 18971310
references.citation: Nature. 2010 Oct 28;467(7319):1099-103
references.pmid: 20981099
references.citation: Am J Hum Genet. 2007 Sep;81(3):559-75
references.pmid: 17701901