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Summary of software used in this manuscript
| Software | Version | Reference |
|---|---|---|
|
| ||
| minimap2 | 2.24-r1122 | H. Li 2018 |
| bwa | 0.7.17-r1188 | H. Li 2013 |
| samtools | 1.16 | H. Li et al. 2009 |
| bcftools | 1.16 | Danecek et al. 2021 |
| clairS | 0.1.16 | Zheng, Su, et al. 2023 |
| mutect2 | 4.4.0.0 | Benjamin et al. 2019 |
| whatshap | 1.7 | Patterson et al. 2015 |
| bedtools | 2.30.0 | Quinlan and Hall 2010 |
| snakemake | 7.19.1 | Köster and Rahmann 2018 |
