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Table 4 General comparison of NRY haplogroup classification tools

From: Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data

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

  1. 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