WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using whole-genome data.
gcc.py is influenced by X and Y chromosomes in a possibly slightly negative way:
Both sex chromosomes are taken into account to determine the LOESS fit on the data, which may negatively influence the fit on the autosomal chromosomes. Removal of the sex chromosomes prior to fitting the curves, while applying the LOESS fit using interpolation on them afterwards would fix this problem.
The effect is extremely minor but depends on fetal fraction. Increasing reads to ChrY at the cost of ChrX however does make this issue worse, although only extremely slightly (quickly estimated: less than 0.25% influence on values per bin at all).
gcc.py is influenced by X and Y chromosomes in a possibly slightly negative way: Both sex chromosomes are taken into account to determine the LOESS fit on the data, which may negatively influence the fit on the autosomal chromosomes. Removal of the sex chromosomes prior to fitting the curves, while applying the LOESS fit using interpolation on them afterwards would fix this problem. The effect is extremely minor but depends on fetal fraction. Increasing reads to ChrY at the cost of ChrX however does make this issue worse, although only extremely slightly (quickly estimated: less than 0.25% influence on values per bin at all).