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QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
2015 BMC Bioinformatics  
When the sequencing is done at high coverage depth ("deep sequencing"), low frequency variants can be detected.  ...  distinguish true single nucleotide variants from sequencing errors based on the estimated SNV probability.  ...  Acknowledgements The authors would like to thank the team members who conducted the Illumina lab experiments, and acknowledge Herwig Van Marck for his insights at the start of the project.  ... 
doi:10.1186/s12859-015-0812-9 pmid:26554718 pmcid:PMC4641353 fatcat:mksjzk4765c2rigp45ao4tbjem