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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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Is there any parameter to determine sex in delly cnv? #384

Open zyxNo1 opened 4 months ago

zyxNo1 commented 4 months ago

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 commented 1 month ago

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.