Table 1.
Basic characteristics of methods used in this study
| Tool | Input | Output | VCF FORMAT Field | Ver. | Ref. | URL |
|---|---|---|---|---|---|---|
| BCFtools | GEN, BCF, VCF, HAPS | BCF, VCF | GT, PL, GL, GQ, GP | 1.6 | PMID: 21,903,627 | http://samtools.github.io/bcftools/bcftools.html |
| QCTOOL | GEN, BGEN, VCF | GEN, VCF | GT, GP | 1.4 | doi: 10.1101/308296 | http://www.well.ox.ac.uk/~gav/qctool/#overview |
| GEN2VCF | GEN, BGEN | VCF | GT, GP, DS | 1.0 | – | https://bitbucket.org/4shin/division-of-genome-research/src/master |
| Oncofunco | GEN | VCF | DS | – | – | https://github.com/oncogenetics/oncofunco |