Table 7.
Computational tools developed by the BSMN Collaborators that are publicly available for community use.
| Code Availability - Repositories and Tools | ||
|---|---|---|
| Computational Tool | Repository | Description |
| BSMN Pipeline8 | https://github.com/bsmn/bsmn-pipeline | A pipeline for aligning and calling variants for the BSMN data. |
| CNVpytor50 | https://github.com/abyzovlab/CNVpytor | A tool for copy number alteration and allelic imbalance analyses. |
| MosaicForecast9 | https://github.com/parklab/MosaicForecast/ | A machine-learning pipeline for finding mosaic SNVs without the need for a control via phasing and random forest modeling. |
| Panel of Normals mask8 | 10.5281/zenodo.4321679 | A panel of normals filter mask for detecting false positives mosaic SNVs. Generated using 30X WGS data from the 10000 Genomes Project. |
| Phase Mosaic10 | https://bitbucket.org/donald_freed/phase-mosaic/src/master/ | A tool to determine if de novo variants are mosaic using phasing of local heterogeneous haplotypes. |
| Find Denovo10 | https://github.com/pevs/find_denovo | A tool for parsing putative de novo variants from a VCF or BCF file. |
| RetroSom11 | https://github.com/XiaoweiZhuJJ/RetroSom | A machine-learning tool for detecting LINE-1 insertions in high depth WGS data. |
| DeepMosaic12 | https://github.com/Virginiaxu/DeepMosaic | A machine-learning tool for visualizing and predicting SNV mosaicism without controls. |
| PySlavSeq13. | https://github.com/apuapaquola/pyslavseq | A tool for working with SLAV-seq data. |
| Longboard13 | https://github.com/PatrickJReed/Longboard | A machine-learning pipeline for detecting LINE-1 insertions in SLAV-seq data. |