Y haplogroup

The paternal line can be narrowed via a few well-placed markers along the tree. Each confirmed derived marker pushes the assignment deeper into a branch, because in the non-recombining part of the Y mutations accumulate in an ordered sequence. Genome evaluates a fixed panel of known ISOGG Y-SNP positions instead of re-sequencing the entire Y, since full Y resequencing is not available for every sample. An existing BAM file is therefore enough to sketch the path through the main branches and subclades.

Genome works in three steps without a dedicated external tool for the Y tree. First it creates a haploid-called Y VCF from the BAM file (bcftools mpileup followed by bcftools call with ploidy 1 on the Y contig). Then it reads a fixed panel of known ISOGG Y-SNP markers position by position with bcftools query and counts a marker as a hit when the expected derived (ALT) allele with a supporting genotype is present. Finally it selects the deepest matching marker as the probable haplogroup; the result lists all detected markers together with a note on the method.

The Y chromosome contains many repetitive and palindromic regions where short reads cannot be placed unambiguously, so coverage and calling confidence vary strongly by locus. A fixed marker panel covers only the defined branches: if the decisive SNP is missing due to thin coverage, the assignment stays coarser or empty. The method therefore describes the probable main lineage, not every fine subclade that a full Y sequencing run against a comprehensive tree would resolve. Resolution depends directly on coverage, data quality, and the number of informative markers in the panel.

The Y haplogroup applies only to the paternal line and only to samples with a Y chromosome. It describes ancestry, not traits or health. With sparse coverage or missing panel markers the assignment stays coarser or may come out empty. The result is technical evidence from defined markers, not a definitive phylogenetic placement against the complete tree.