XYalign: Version 1.1.4

<p>The high degree of similarity between gametologous sequences on the sex chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) quickly infers sex chromosome ploidy in NGS data, (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across chromosomes.</p