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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...was set to 2, and the minimum SV size was set to 30 bp, although the final variant calls were a more stringent subset of these requiring higher read support and larger sizes. PBSV was run with default settings. For Illumina/10xG reads, we used SvABA v FH134, LUMPY v 0.2.13, Manta v 1.5.0, GROC-SVs v 0...
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Method: Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples
- Sergey Aganezov and
- Benjamin J. Raphael
Genome Res. September 2020 30: 1274-1290; Published in Advance September 4, 2020, doi:10.1101/gr.256701.119
...single-nucleotide mutations through copy number aberrations and large-scale rearrangements (Stratton et al. 2009; Garraway and Lander 2013; Vogelstein et al. 2013; Raphael et al. 2014). Whole- sequencing of tumor samples has enabled the detection of all classes of somatic mutations; however, specialized...

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