I have 2 cell lines that have unusual karyotypes. One is a mixture of diploid and tetraploid cells (in average it is a triploid) and the other has chromosome number of ranging from 85 to 102.
I was wondering the following:
1) what kind of damage will I have if I use non-standard diploid samples as the reference?
2) is there a way that I can calculate the non-integer copy number variation? In my case, The average copy number of a cell line can very well be 3.8 as it is a mixture.
Another question about the sex of the sample:
I got the following output from a male sample using a male reference sample. and I specified --male-reference for the sample.
Relative log2 coverage of chrX=-1.23, chrY=-4.56 (maleness=14.1 x 0.0678 = 0.954) --> assuming female
I have 2 cell lines that have unusual karyotypes. One is a mixture of diploid and tetraploid cells (in average it is a triploid) and the other has chromosome number of ranging from 85 to 102.
I was wondering the following:
1) what kind of damage will I have if I use non-standard diploid samples as the reference? 2) is there a way that I can calculate the non-integer copy number variation? In my case, The average copy number of a cell line can very well be 3.8 as it is a mixture.
Another question about the sex of the sample: I got the following output from a male sample using a male reference sample. and I specified --male-reference for the sample.
Relative log2 coverage of chrX=-1.23, chrY=-4.56 (maleness=14.1 x 0.0678 = 0.954) --> assuming femaleCould you please kindly explain the output above?
Thank you very much, Dingwen