ChASM (Chromosomal Aneuploidy Screening Methodology) is a statistically rigorous Bayesian approach for screening data sets for autosomal and sex chromosomal aneuploidies. An associated R implementation RChASM, is available to implement this approach. RChASM takes as input the number of (de-duplicated) reads mapping to chromosomes 1-22 and the X and Y chromosomes, and models these using a Dirichlet-multinomial distribution. From this, RChASM returns posterior probabilities of sex chromosomal karyotypes (XX, XY, XXY, XYY, XXX and X) and full autosomal aneuploidies (trisomy 13, trsomy 18 and trisomy 21). 

RChASM also returns two diagnostic statistics: (i) a posterior probability addressing whether contamination between XX and XY may explain the observed sex chromosomal aneuploidy, and (ii) a chi-squared statistic measuring whether the observed read counts are significantly divergent from the underlying distribution (and may represent abnormal sequencing/quality issues).

Currently RChASM is in an alpha build phase, with the associated manuscript in preparation, and should be used with this in mind. Due to this, please feel free to email me with any questions you might have.

Work done with my colleagues: