Dataset Information

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.

ABSTRACT:

Background

The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious problem of computation bottlenecks, resulting in some long tail tasks when performing on large datasets. This prevents high scalability on clusters of multi-node and multi-core, and leads to long runtime and inefficient usage of computing resources. Thus, a high scalable tool which could run in distributed environment will be highly useful to accelerate variant calling on large scale genome data.

Results

In this paper, we present ADS-HCSpark, a scalable tool for variant calling based on Apache Spark framework. ADS-HCSpark accelerates the process of variant calling by implementing the parallelization of mainstream GATK HaplotypeCaller algorithm on multi-core and multi-node. Aiming at solving the problem of computation skew in HaplotypeCaller, a parallel strategy of adaptive data segmentation is proposed and a variant calling algorithm based on adaptive data segmentation is implemented, which achieves good scalability on both single-node and multi-node. For the requirement that adjacent data blocks should have overlapped boundaries, Hadoop-BAM library is customized to implement partitioning BAM file into overlapped blocks, further improving the accuracy of variant calling.

Conclusions

ADS-HCSpark is a scalable tool to achieve variant calling based on Apache Spark framework, implementing the parallelization of GATK HaplotypeCaller algorithm. ADS-HCSpark is evaluated on our cluster and in the case of best performance that could be achieved in this experimental platform, ADS-HCSpark is 74% faster than GATK3.8 HaplotypeCaller on single-node experiments, 57% faster than GATK4.0 HaplotypeCallerSpark and 27% faster than SparkGA on multi-node experiments, with better scalability and the accuracy of over 99%. The source code of ADS-HCSpark is publicly available at https://github.com/SCUT-CCNL/ADS-HCSpark.git .

SUBMITTER: Xiao A

PROVIDER: S-EPMC6376756 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.

Xiao Anghong A Wu Zongze Z Dong Shoubin S

BMC bioinformatics 20190214 1

<h4>Background</h4>The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious problem of computation bottlenecks, resulting in some long tail tasks when performing on large datasets. This prevents high scalability on clusters of multi-node and multi-cor ...[more]

PMID: 30764760

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Dataset Information

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.

Background

Results

Conclusions

Publications

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.

Similar Datasets

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