I’ll feature major software releases here, but I have much more code available on Github.
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) aids in the inference of sex chromosome content using 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. Moreover, XYalign can be leveraged to examine a variety of other phenomena on both sex chromosomes and autosomes (e.g., aneuploidy, etc.).