Supporting data for "Halvade Somatic: Somatic Variant Calling with Apache Spark"

The 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 also the detection of low-frequency variants is 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. <br>We 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 19.5h compared to a runtime of 84.5h for the original pipeline, a speedup of 4.3x. Runtime can be further decreased by scaling to multiple nodes while retaining a high parallel efficiency, e.g., we observe a runtime of 1h 21min using 16 nodes, an additional speedup of 14.4x. The somatic variants called by Halvade Somatic match those obtained by the original GATK/Mutect2 pipeline to a very high degree. Halvade Somatic supports variant calling from both whole genome sequencing (WGS) as well as whole exome sequencing (WES) data and also supports Strelka2 as an alternative or complementary variant calling tool within its pipeline. We provide a Docker image to facilitate single node deployment. Halvade Somatic can be executed on a wide variety of compute platforms, including the Amazon EC2 and Google Cloud. <br>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.