KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Human sperm, blood, and saliva samples | See Experimental Model and Subject Details | ID01-ID17 |
| Chemicals, peptides, and recombinant proteins | ||
| AMPure XP Beads | Beckman Coulter | A63882 |
| PureCeption™ 100% Isotonic Solution | Sage/Origio | ART-2100 |
| QUINN’S™ Sperm Washing Medium | Sage/Origio | ART-1006 |
| RLT lysis buffer | Qiagen | 40724 |
| Bond-Breaker TCEP solution | Thermo Scientific | 77720 |
| stainless steel beads with 0.2 mm diameter | Next Advance | SSB02 |
| GoTaq Colorless Master Mix | Promega | M7832 |
| Exonuclease I | New England Biolabs | M0293S |
| Shrimp Alkaline Phosphatase | New England Biolabs | M0371S |
| Critical Commercial Assays | ||
| AllPrep DNA/RNA Mini Kit | Qiagen | 80204 |
| KAPA HyperPrep PCR-Free Library Prep kit | Roche | KK8505 |
| KAPA Library Quantification Kits for Illumina platforms | Roche/KAPA Biosystems | KK4824 |
| Illumina SBS kits | Illumin | 20012866 |
| Qubit dsDNA High Sensitivity kit | Thermo Fisher Scientific | Q33231 |
| Deposited Data | ||
| 200× WGS and TAS data | Sequence Read Archive (SRA) | PRJNA588332 |
| 300× WGS and TAS data | Sequence Read Archive (SRA) | PRJNA660493 |
| Software and Algorithms | ||
| Picard v 2.20.7 | “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. | https://broadinstitute.github.io/picard/ |
| BWA v 0.7.8 | (Li and Durbin, 2009) | http://bio-bwa.sourceforge.net/ |
| Circos v0.69–6 | (Krzywinski et al., 2009) | http://circos.ca/ |
| SAMtools v 1.7 | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| GATK v 3.8–1, v4.0.4 | (McKenna et al., 2010) | https://gatk.broadinstitute.org/hc/en-us |
| BCFtools v 1.10.32 | (Li et al., 2009) | http://samtools.github.io/bcftools/ |
| BEDTools v 2.27.1 | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io/en/latest/ |
| MosaicForecast v 8–13-2019 | (Dou et al., 2020) | https://github.com/parklab/MosaicForecast |
| Mutect2 v4.0.2 | (Benjamin et al., 2019) | https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2 |
| Strelka2 v 2.9.2 | (Kim et al., 2018) | https://github.com/Illumina/strelka |
| Pysam v 0.11.2.2 | (Li et al., 2009) | https://github.com/pysam-developers/pysam |
| Pysim | (Xia et al., 2017) | https://github.com/aldebjer/pysim |
| PLINK v 1.90b6.16 | (Purcell et al., 2007) | http://zzz.bwh.harvard.edu/plink/ |
| gnomAD v 2.1.1 | (Karczewski et al., 2020) | https://gnomad.broadinstitute.org/ |
| Python v 3.6.8 and v 3.7.3 | Python Software Foundation | https://www.python.org/downloads/ |
| SciPy v 1.3.1 | Community library project | https://www.scipy.org/ |
| sklearn v 0.20.1 | scikit-learn project | https://scikit-learn.org/stable/ |
| R v 3.5.1 | R Core Team | https://www.r-project.org/ |
| FSA v 0.8.30 | http://derekogle.com/FSA/authors.html | https://cran.r-project.org/web/packages/FSA/index.html |
| pingouin v 0.3.5 | https://pingouin-stats.org/ | |
| pandas v 0.24.2 | the pandas development team | https://pandas.pydata.org/ |
| seaborn v 0.9.0 | Michael Waskom | https://seaborn.pydata.org/ |
| NumPy v 1.16.2 | the NumPy project | http://numpy.org/ |
| matplotlib v 3.1.1 | https://ieeexplore.ieee.org/document/4160265 | https://maplotlib.org/ |
| Primer 3 | (Untergasser et al., 2012; Untergasser et al., 2007) | http://primer3.org/manual.html |
| Other | ||
| Cell counting chamber | Sigma-Aldrich | BR717805-1EA |
| Disruptor Genie | Scientific Industries | SI-238I |
| 1.5 ml microcentrifuge tube | USA Scientific | 1615-5500 |
| Covaris microtube system | Covaris | SKU 520053 |
| Bio-IT platform | Illumina | DRAGEN |
| Next generation sequencer | Illumina | NovaSeq 6000 |
| Next generation sequencer | Illumina | HiSeq 4000 |
| focused-ultrasonicator | Covaris | E220 |
| Plate reader | Eppendorf | PlateReader AF2200 |
| Qubit 3 Fluorometers | Thermo Fisher | Q33216 |
| Deposited Data | ||
| Raw and analyzed data | This paper | SRA: PRJNA660493 |
| Raw and analyzed data | (Breuss et al., 2020a) | SRA: PRJNA588332 |