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Calling modes

GATK-SV offers two different modes for SV calling. Users should carefully review the following sections to determine which mode is appropriate for their use case.

Single-sample mode​

GATK-SV can perform SV calling on individual samples. In this mode, a sample is jointly called against a fixed reference panel of 156 high-quality samples from the 1000 Genomes Project. Single-sample mode is a good option for the following use cases:

  • Studies involving fewer 100 samples
  • Studies with rolling data delivery, i.e. in small batches over time

Users should also consider that the single-sample mode is provided as a single workflow and is therefore considerably simpler to run than joint calling. However, it also has higher compute costs on a per-sample basis and will not be as sensitive as joint calling with larger cohorts. Additionally, SV quality will be best when the case sample closely resembles the samples in the reference panel in terms of sequencing depth, sample quality, and library preparation.

Joint calling mode​

GATK-SV can also perform joint calling on a set of samples. Users may opt for this mode in the following use cases:

  • Studies involving at least 100 samples
  • When maximum sensitivity is desired
  • Data sets that are technically heterogeneous, i.e. with strong batch effects, or are very different from the single-sample mode reference panel

Joint calling has the advantage of increasing SV discovery sensitivity and providing allele frequency estimates, and there are some features, such as genotype recalibration and filtering and in-depth QC plotting, that are only available in joint calling mode. However, this pipeline is considerably more complex to execute than the single-sample mode, requiring sample batching and the execution of several individual modules.

Related content​

More information on single-sample and joint calling can be found in the Execution section.