Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Software, algorithm | GATK | (Van der Auwera et al., 2013; Zhang et al., 2017) | ||
| Software, algorithm | HLA-VBSeq | (Nariai et al., 2015) | ||
| Software, algorithm | SAMtools version 1.2 | (Li et al., 2009) | ||
| Software, algorithm | STAR (2.5.0a) | (Dobin et al., 2013; Harrow et al., 2012) | ||
| Software, algorithm | RSEM (1.2.20) | (Li and Dewey, 2011) | ||
| Software, algorithm | bcftools | (Li et al., 2009) | ||
| Software, algorithm | lmekin (coxme package) | R 3.5.1 | ||
| Software, algorithm | MBASED | (Mayba et al., 2014) | ||
| Software, algorithm | coloc.abf (coloc package) | R 3.5.1 (Giambartolomei et al., 2014) |