Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| 1000 Genomes project data | The International Genome Sample Resource | RRID: SCR_006828 |
| ExAC | Lek et al. 2016 | https://gnomad.broadinstitute.org/ |
| gnomAD v2.1.1 | Karczewski et al. 2020 | https://gnomad.broadinstitute.org/ |
| Partners HealthCare Biobank | Mass General Brigham | RRID:SCR_00131 6 |
| Trans-Omics for Precision Medicine (TOPMed) program | NHLBI Trans-Omics for Precision Medicine | RRID:SCR_01567 7 |
| TCGA whole-exome sequencing | Genomic Data Commons | RRID: SCR_014555 |
| TCGA SNP 6.0 array | TCGA legacy archive | https://portal.gdc.cancer.gov/legacy-archive/search/f |
| TCGA clinical and subtype data | Genomic Data Commons | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Additional somatic validation datasets | GENIE v11.1 | https://www.aacr.org/professionals/research/aacr-project-genie/ |
| Software and algorithms | ||
| PLINK v2.0 | Chang et al., 2015 | https://www.cog-genomics.org/plink/2.0/ |
| MuTect | Cibulskis et al. 2013 | https://software.broadinstitute.org/cancer/cga/mutect_download |
| Picard | Broad Institute | http://broadinstitute.github.io/picard/ |
| GATK | Poplin et al., 2017 | https://gatk.broadinstitute.org/hc |
| Burrows Wheeler Aligner | Li and Durbin, 2009 | http://bio-bwa.sourceforge.net/ |
| Bcftools v1.10.2 | Danecek et al., 2021 | https://samtools.github.io/bcftools/bcftools.html |
| VCFtools v0.1.15 | Danecek et al., 2011 | https://vcftools.github.io/ |