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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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setting gender to XY #73

Closed lmy06 closed 6 years ago

lmy06 commented 6 years ago

Hi, I was using ascatNGS with WGS datas. I just find out if I set the gender to XY, the CNV segment result will show a deletion in chrX. Even the data is from a female, if I set the gender=XY, there will be a deletion in the chrX. And the other chromosomes' CNV segments were different between setting gender to XY or XX. I'm wondering why this happens?

keiranmraine commented 6 years ago

Issues with the underlying ASCAT algorithm should be raised on their repository detailed in the README. You should either set gender correctly for the samples or specify gender as 'L' for the code to determine it using Y specific SNP loci.