Table 4.
General comparison of NRY haplogroup classification tools
| Tool | Version | Programming Language | Supported Input Format | Sample Input form | Number of Markers | Supported Reference |
|---|---|---|---|---|---|---|
| Y-LineageTracker | 1.3.0 | Python | VCF, BAM/CRAM | Multiple | 74, 570 | hg19, hg38 |
| HaploGrouper | 1.0 | Python | VCF | Multiple | 71, 406 | hg19, hg38 |
| AMY-Tree | 2.0 | Perl | VCF-like | Single | 5, 925 | hg18, hg19 |
| Yleaf | 2.2 | Python | FASTQ, BAM/CRAM | Single | 65, 459 | hg19, hg38 |
| clean-tree | 2.0 | Python, R | BAM | Single | 539 | hg19 |
General comparison of currently available NRY haplogroup classification tools. The sample input form means whether the tool can take multiple files or a single file as input to perform analysis