We are using lpWGS data to analyzed the CNV status of the genome, and plot the Log2Ratio, using samples from misscarriage ones.
ichorCNA was used. However, we found the CNV plot was roughly noised across the genome, which is largely different from the plot offered in the paper, although those plots were generated from ctDNA samples.
I am wondering any other tools can be applied? Or any parameters can be tuned to normalized or denoise the data?