OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow.

ABSTRACT:

Background

The advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology. The computational task of detecting and annotating sequence differences of a target dataset between a reference genome is known as "variant calling". Typically, this task is computationally involved, often combining a complex chain of linked software tools. A major player in this field is the Genome Analysis Toolkit (GATK). The "GATK Best Practices" is a commonly referred recipe for variant calling. However, current computational recommendations on variant calling predominantly focus on human sequencing data and ignore ever-changing demands of high-throughput sequencin

SUBMITTER: Bathke J 

PROVIDER: S-EPMC8361789 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature