Searching thousands of genomes to classify somatic and novel structural variants using STIX.
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ABSTRACT:
SUBMITTER: Chowdhury M
PROVIDER: S-EPMC9007735 | biostudies-literature | 2022 Apr
REPOSITORIES: biostudies-literature
Publications
Searching thousands of genomes to classify somatic and novel structural variants using STIX.
Chowdhury Murad M Pedersen Brent S BS Sedlazeck Fritz J FJ Quinlan Aaron R AR Layer Ryan M RM
Nature methods 20220408 4
Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele freque ...[more]
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