Published August 20, 2020
| Version 1.0.0
Dataset
Open
PopDel identifies medium-size deletions jointly in tens of thousands of genomes - Variant call sets
Authors/Creators
- 1. Regensburg Center for Interventional Immunology (RCI); Charité - Universitäsmedizin Berlin; Berlin Institute of Health (BIH)
Description
This data set contains the variant calls sets generated by different tools for the benchmarks in the paper PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes. It includes the VCFs/BCFs for the following test cases:
- Random deletion simulation on up to 1000 chromosome 21 samples
- 1000 Genomes Project deletions inserted into simulated chromosomes 17 to 22 of up to 500 samples
- HG001 (NA12878)
- Trio of HG002 + HG003 + HG004
- Polaris Diversity cohort
- Polaris Kids cohort
Further, the long and short read reference call sets for HG001 are provided. For HG002 the reference call set and the high confidence regions by the Genome in a Bottle consortium are provided.
For details on how the files have been created, please refer to the paper and the script repository on GitHub.
Notes
This work was funded by the German Federal Ministry of Education and Research under grant number 031L0180.
Files
Additional details
Related works
- Is supplement to
- Journal article: 10.1038/s41467-020-20850-5 (DOI)
- Preprint: 10.1101/740225 (DOI)
References
- Auton, A., Abecasis, G., Altshuler, D. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
- Zook, J.M., Chapman, B., Wang, J. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol 32, 246–251 (2014).
- Zook, J.M., Hansen, N.F., Olson, N.D. et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol (2020).