PUBLICATION.md

SViCT: Structural Variant detrction in Circulating Tumor DNA

If you use SViCT in your publication, please cite the following article:

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA. Alexander R Gawroński, Yen-Yi Lin, Brian McConeghy, Stephane LeBihan, Hossein Asghari, Can Koçkan, Baraa Orabi, Nabil Adra, Roberto Pili, Colin C Collins, S Cenk Sahinalp, Faraz Hach. Nucleic Acids Res. 2019 Feb 13. doi: 10.1093/nar/gkz067

Simulation Datasets Used for Evaluation

Please check this link to download the simulation datasets that we used for evaluating SViCT. The folder contains 7 data files:

1. sim.150.sorted.bam: BAM file containing simulated 2*150bp cfDNA reads from a Venter genome with inserted SVs
2. sim.100.sorted.bam: BAM file containing simulated 2*100bp cfDNA reads from a Venter genome with inserted SVs
3. sim.75.sorted.bam: BAM file containing simulated 2*75bp cfDNA reads from a Venter genome with inserted SVs
4. Homo_sapiens.GRCh38.87.dna.chromosomes.fa: GRCh38 reference genome for the above mappings.
5. sim.150.vcf: Predictions results for sim.150.sorted.bam
6. sim.100.vcf: Predictions results for sim.100.sorted.bam
7. sim.75.vcf: Predictions results for sim.75.sorted.bam

We also provide a checksum file md5.sum for checking file integrity.

Existing SV callers Used in Performance Comparisons

The versions of other SV callers we use in the publication are

1. Lumpy2 0.2.13
2. GRIDSS 1.4.3
3. Socrates 1.13.1
4. Pindel 0.2.5
5. Delly2 0.7.8

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