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chevron_left Structural variant detection Deletion detection Insertion detection chevron_right
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SWAN specifications

Information


Unique identifier OMICS_12197
Name SWAN
Alternative name Statistical Structural Variant Analysis for NGS
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, R
Computer skills Advanced
Stability Stable
Requirements
GCC, Samtools, R::RcppArmadillo, Rcpp, BH, data.table, devtools, digest, hash, methods, optparse, parallel, plyr, robustbase, sets, stringr, zoo, BioConductor::Biobase, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools
Maintained Yes

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Documentation


Maintainer


  • person_outline Li C. Xia <>

Publication for Statistical Structural Variant Analysis for NGS

SWAN in publication

PMCID: 5870608
PMID: 28881988
DOI: 10.1093/bioinformatics/btx254

[…] and also incorporates the split-read sequence signature () to discover and then genotype common sequence insertions within a large cohort of samples. using “soft-clipped” reads, another algorithm swan () can only find breakpoints of long insertions without providing its content., in this paper, we present pamir, a new tool to provide exact breakpoint positions, sequence contents, […]

SWAN institution(s)
Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Statistics, the Wharton School, University of Pennsylvania, Philadelphia, PA, USA; Stanford Genome Technology Centre, Stanford University, Palo Alto, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA
SWAN funding source(s)
National Institutes of Health (NIH) [2R01HG006137-04 and P01HG00205ESH] and National Science Foundation (NSF)

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