Halvade somatic: Somatic variant calling with Apache Spark.

ABSTRACT:

Background

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 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.

Findings

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

SUBMITTER: Decap D 

PROVIDER: S-EPMC8756192 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature