I am looking for any software which can correct the GC-Bias in the BAM file and provides the output as BAM.
I know that deeptools (correctGCBias) does the exactly same job, but the output of the deeptools is variable in each run.
So, I am looking for more specific tool.
Basically, I want to count the sequence reads for each chromosome in NIPT (low depth, WGS sample) BAM file after the GC-Bias correction.
Many LOESS based or R-based GC-bias correction methods are available, but they provides the output as normalized data, not as total number of reads in each chromosome/ specified region.