XYalign: Inferring and Correcting for Sex Chromosome Ploidy in Next-Generation Sequencing Data

Authors:Timothy Webster, Madeline Couse, Bruno Grande, Eric Karlins, Tanya Phung, Phillip Richmond, Whitney Whitford, Melissa Wilson Sayres
Date:Apr 11, 2019
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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.

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