title: BAM-matcher: a tool for rapid NGS sample matching.
abstract: The standard method used by high-throughput genome sequencing facilities for detecting mislabelled samples is to use independently generated high-density SNP data to determine sample identity. However, as it has now become commonplace to have multiple samples sequenced from the same source, such as for analysis of somatic variants using matched tumour and normal samples, we can directly use the genotype information inherent in the sequence data to match samples and thus bypass the need for additional laboratory testing. Here we present BAM-matcher, a tool that can rapidly determine whether two BAM files represent samples from the same biological source by comparing their genotypes. BAM-matcher is designed to be simple to use, provides easily interpretable results, and is suitable for deployment at early stages of data processing pipelines.
  
  
  
  BAM-matcher is licensed under the Creative Commons by Attribution license, and is available from: https://bitbucket.org/sacgf/bam-matcher
  
  
  
  Supplementary data are available at Bioinformatics online.
  
  
  
  paul.wang@sa.gov.au.
authors.affiliation: Department of Genetics and Molecular Pathology, and ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.
authors.forename: Paul P S
authors.initials: PP
authors.lastname: Wang
authors.affiliation: Department of Genetics and Molecular Pathology, and ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia, School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia.
authors.forename: Wendy T
authors.initials: WT
authors.lastname: Parker
authors.affiliation: Department of Genetics and Molecular Pathology, and School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia, School of Biological Sciences and School of Medicine, University of Adelaide, Adelaide, Australia.
authors.forename: Susan
authors.initials: S
authors.lastname: Branford
authors.affiliation: ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia, School of Biological Sciences and.
authors.forename: Andreas W
authors.initials: AW
authors.lastname: Schreiber
mesh_terms: D016678:Genome; D005838:Genotype; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software