Appreci8: a pipeline for precise variant calling integrating 8 tools.

ABSTRACT:

Motivation

The application of next-generation sequencing in research and particularly in clinical routine requires valid variant calling results. However, evaluation of several commonly used tools has pointed out that not a single tool meets this requirement. False positive as well as false negative calls necessitate additional experiments and extensive manual work. Intelligent combination and output filtration of different tools could significantly improve the current situation.

Results

We developed appreci8, an automatic variant calling pipeline for calling single nucleotide variants and short indels by combining and filtering the output of eight open-source variant calling tools, based on a novel artifact- and polymorphism score. Appreci8 was trained on two data sets from

SUBMITTER: Sandmann S 

PROVIDER: S-EPMC6289140 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature