Is there any parameter to determine sex in delly cnv?

[zyxNo1]

Is there any parameter to determine sex when calling cnv in human? I noticed the parameter "--haploid-chr arg haploid chromosomes, e.g. chrX,chrY". Could this be helpful?

[tobiasrausch]

You can simply run delly cnv with default options and then plot all chromosomes. For humans, male samples should then show a copy-number of 1 for chrX and females a copy-number of 2.
The --haploid-chr option is only necessary for cancer samples with imperfect purity (normal cell contamination) where you can still use default options to determine sex but to adjust for normal cell contamination (option -p) you need to tell delly which chromosomes are haploid.

[sounkou-bioinfo]

hi @tobiasrausch
thanks for this great tool !
i have a question on this point, does delly call cnv on Y or X chromosome for male samples ? is sex inferred in the pipeline ? I am referring to the cases where there is for example a duplication of segments on the Y chromosome for a XY sample (WGS, Germeline).
Another point, would you expect a good accuracy on low coverage WGS or Target sequencing (with target capture regions defined) data ?
Also, are there plans for a documentation of the cnv calling algorithm ?
Thank you