Abstract
BackgroundThe estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data.ResultsWe introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process.ConclusionThe program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).
Highlights
Being able to estimate how closely related 2 individuals are and whether they are inbred is important in several different fields ranging from conservation genetics to medical genetics
The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data
The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics
Summary
Being able to estimate how closely related 2 individuals are and whether they are inbred is important in several different fields ranging from conservation genetics to medical genetics. For this purpose, numerous coefficients, such as the kinship coefficient and inbreeding coefficients, have been defined and many programs for estimating these coefficients have been proposed. J9), and their corresponding frequencies in the genome of 2 individuals are called the condensed Jacquard coefficients (here denoted J1, J2, ..., J9) These condensed coefficients provide a comprehensive description of the common ancestry between 2 individuals that can be used to infer their familial relationship. The program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF)
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.
