Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery

Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of uncertainties related to gap and alignment ambi...

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Bibliographic Details
Published in:Genome Biology 2020-04, Vol.21 (1), p.98-25, Article 98
Main Authors: Köster, Johannes, Dijkstra, Louis J, Marschall, Tobias, Schönhuth, Alexander
Format: Article
Language:English
Subjects:
Accuracy
Bayes Theorem
Bayesian latent variable model
Cancer
Evolution, Molecular
FDR control
Gene Frequency
Genomes
Humans
INDEL Mutation
Mathematical models
Method
Mutation
Neoplasms - genetics
Probability
Sequence Analysis
Somatic
Tumor/normal
Variant calling
Workflow
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Summary:Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of uncertainties related to gap and alignment ambiguities, twilight zone indels, cancer heterogeneity, sample purity, sampling, and strand bias. We provide a unifying statistical model whose dependency structures enable accurate quantification of all inherent uncertainties in short time. Consequently, false discovery rate (FDR) in somatic indel discovery can now be controlled at utmost accuracy, increasing the amount of true discoveries while safely suppressing the FDR.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-01993-6