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Table 1 Functions implemented in Y-LineageTracker

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

Function

Command

Description

NRY haplogroup classification

Classify

Classify NRY haplogroups from BAM or VCF file

Clustering analysis

Cluster

Perform clustering analysis for NRY haplogroups

Phylogeny analysis

Phylo

Perform phylogeny analysis for NRY haplogroups

Y-STR genotyping

Genostr

Genotype Y-STRs from BAM or VCF indels

Network analysis

Net

Perform network analysis for Y-STR haplotypes

Statistical analysis

Stat

Perform statistical analysis for Y-STR haplotypes

Time estimation

Time

Estimate NRY haplogroup divergence time

Tmrca

Estimate TMRCA of Y-STR haplotypes

  1. Y-DNA analysis functions implemented in Y-LineageTracker. Each function is corresponding to a command