Best practices for improving alignment and variant calling on human sex chromosomes.

ABSTRACT: Sex chromosome complement is the largest karyotypic variation observed in humans. X and Y chromosomes were once a pair of homologous autosomes. Although chromosome X and Y differentiated from one another, they still share high levels of sequence similarity in some regions, like the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The sex chromosomes violate some assumptions of autosomal pairs, but are not always processed separately in genomics analyses. Here, we undertook a simulation study to assess the effects of standard autosomal versus sex chromosome complement-informed alignment, variant calling, and variant filtering strategies on variants detected on the human sex chromosomes. We find that aligning samples to a reference genome informed by the sex chromosome compl

SUBMITTER: Taravella Oill AM 

PROVIDER: S-EPMC12190741 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature