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 NG

SUBMITTER: Lee S 

PROVIDER: S-EPMC5499645 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature