ExaScience Life Lab, imec, Leuven, Belgium.
Department of Information Technology, Ghent University - imec, Ghent, Belgium.
PLoS One. 2021 Feb 4;16(2):e0244471. doi: 10.1371/journal.pone.0244471. eCollection 2021.
We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK4. This makes elPrep 5 a suitable drop-in replacement for GATK4 when faster execution times are needed.
我们介绍了 elPrep 5，它更新了 elPrep 框架，用于处理具有变体调用的测序比对/映射文件。elPrep 5 现在可以执行 GATK 变体调用最佳实践所描述的完整管道，该管道包括 PCR 和光学重复标记、按坐标顺序排序、碱基质量评分重新校准以及使用单倍型调用算法进行变体调用。elPrep 5 生成与 GATK4 相同的 BAM 和 VCF 输出，同时通过并行化和合并管道步骤的执行显著减少了运行时间。我们的基准测试表明，elPrep 5 在使用与 GATK4 相同的硬件资源的情况下，将全外显子组和全基因组数据的变体调用管道的运行时间加快了 8-16 倍。这使得 elPrep 5 在需要更快的执行时间时成为 GATK4 的合适替代品。
