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

Sex chromosome aneuploidies are currently estimated to be as common as 1/400 in humans. Atypical ploidy will affect variant calling and measures of genomic variation that are central to most clinical genomic studies. Further, the high degree of similarity between gametologous sequences on the X and Y 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 (DNA and RNA), (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across the sex chromosomes

Additional file 5: Supplementary Figures. of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Figure S1. IGV image and Sanger verification trace files for indel in ARID1B and missense variation in UPF1. Figure S2. UK10K mutation load – counts as per variant annotation type on one patient. Figure S3. Histogram of mutation burden per patient in the UK10K cohort. Figure S4. Pathway interactions showing convergence onto UPP pathway. Figure S5. Plots for CNV distribution for two chromosomes as called by CNAseq. (DOCX 1972 kb

Additional file 1: of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Supplementary Methods - Additional details on methods presented succinctly in main text. (DOCX 53 kb

Additional file 4: Table S3. of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

UK10K study cohorts that comprise the positive control cohort – Table giving descriptions of the study cohorts from the UK10K project that comprised the positive control cohorts and conditions for use. (XLSX 13 kb