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SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.

ABSTRACT: It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.

SUBMITTER: Wang M

PROVIDER: S-EPMC7393490 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.

Wang Mingyi M Luo Wen W Jones Kristine K Bian Xiaopeng X Williams Russell R Higson Herbert H Wu Dongjing D Hicks Belynda B Yeager Meredith M Zhu Bin B

Scientific reports 20200730 1

It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve perfo ...[more]

PMID: 32732891

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Project description:BackgroundThe accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements. For example, calling the somatic variants according to the GATK best practices guidelines requires days of computing time for a typical whole-genome sequencing sample.FindingsWe introduce Halvade Somatic, a framework for somatic variant calling from DNA sequencing data that takes advantage of multi-node and/or multi-core compute platforms to reduce runtime. It relies on Apache Spark to provide scalable I/O and to create and manage data streams that are processed on different CPU cores in parallel. Halvade Somatic contains all required steps to process the tumor and matched normal sample according to the GATK best practices recommendations: read alignment (BWA), sorting of reads, preprocessing steps such as marking duplicate reads and base quality score recalibration (GATK), and, finally, calling the somatic variants (Mutect2). Our approach reduces the runtime on a single 36-core node to 19.5 h compared to a runtime of 84.5 h for the original pipeline, a speedup of 4.3 times. Runtime can be further decreased by scaling to multiple nodes, e.g., we observe a runtime of 1.36 h using 16 nodes, an additional speedup of 14.4 times. Halvade Somatic supports variant calling from both whole-genome sequencing and whole-exome sequencing data and also supports Strelka2 as an alternative or complementary variant calling tool. We provide a Docker image to facilitate single-node deployment. Halvade Somatic can be executed on a variety of compute platforms, including Amazon EC2 and Google Cloud.ConclusionsTo our knowledge, Halvade Somatic is the first somatic variant calling pipeline that leverages Big Data processing platforms and provides reliable, scalable performance. Source code is freely available.

Dataset Information

SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.

Publications

SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.

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