title: NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
abstract: In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies.
  
  
  BACKGROUND
  https://github.com/parklab/NGSCheckMate.
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, South Korea.|SD Genomics Co., Ltd, Seoul, 06336, South Korea.
authors.forename: Sejoon
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Soohyun
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Ouellette
authors.affiliation: Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, South Korea.
authors.forename: Woong-Yang
authors.initials: WY
authors.lastname: Park
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.|Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Eunjung A
authors.initials: EA
authors.lastname: Lee
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.|Ludwig Center at Harvard, Boston, MA 02115, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
mesh_terms: D056915:DNA Copy Number Variations; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D012984:Software