SVCFit benchmark dataset

This page contains all the data required to reproduce the figures included in the publication. The source code for SVCFit and the figures is freely available at https://github.com/KarchinLab/SVCFit. ===================================================================================== In the Figure_1 folder: - input: BED files used for data simulation. - HACk.random.bed is for single-clone simulation. - c1.bed, c2.bed, and c3.bed are for multiple-clone simulation. - allele2.bed is an empty file required by VISOR [1] for simulating heterozygous variants. - multiple_vcfs: VCF files from multiple-clone simulation. - single_vcfs: VCF files from single-clone simulation. - svc_m_rdata: SVclone output from multiple-clone simulation, saved in .RData format. - svc_s_rdata: SVclone output from single-clone simulation, saved in .RData format. - svcfit_time.txt: A text file storing runtime results from SVCFit. - svclone_time.txt: A text file storing runtime results from SVclone. *Figures 1A and 1B: input, single_vcfs, multiple_vcfs, svc_s_rdata, svc_m_rdata *Figure 1C: The data used to create the mixtures is available upon request from the European Genome-phenome Archive (EGAD00001001343). The script used to create the mixtures is available at https://github.com/mcmero/SVclone_Rmarkdown/blob/master/make_insilico_mixtures.sh [2]. *Figure 1D: svcfit_time.txt, svclone_time.txt In the Figure_S folder: - HACk.random.bed: Contains structural variants included in the simulation for read depth analysis. - depth: A folder containing read depth data for each simulation. *Figure S2: HACk.random.bed, depth Reference 1. Bolognini, Davide, Sanders, Ashley, Korbel, Jan O, Magi, Alberto, Benes, Vladimir, and Rausch, Tobias, ‘VISOR: A Versatile Haplotype-Aware Struc-tural Variant Simulator for Short- and Long-Read Sequencing’, Bioinfor-matics, 36/4 (2020), 1267–69 2. Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Corcoran, Niall M., Papenfuss, Tony, et al., "Inferring Structural Variant Cancer Cell Fraction," Nature Communications, 11(1) (2020), 730.