Abstract
BackgroundIdentification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches usually yield high false positive rate.ResultsIn this study, we developed a gradient boosting approach for filtering de novo indels obtained by any computational approaches. Through application on the real genome sequencing data, our approach showed it could significantly reduce the false positive rate of de novo indels without a significant compromise on sensitivity.ConclusionsThe software DNMFilter_Indel was written in a combination of Java and R and freely available from the website at https://github.com/yongzhuang/DNMFilter_Indel.
Highlights
Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices
The standard method refers to that commmly used indel detection methods [5,6,7] are firstly employed to detect indels for all individuals in a trio independently and putative de novo indels are identified by comparing the genotypes of parents and the offspring
The joint calling methods refers to direct detection of de novo indels from the trio, and representative methods include DeNovoGear [8], PhaseByTransmission [9] and TrioDeNovo [10]
Summary
Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. The joint calling methods refers to direct detection of de novo indels from the trio, and representative methods include DeNovoGear [8], PhaseByTransmission [9] and TrioDeNovo [10].
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
