Override sample gender

Question

Override sample gender

Closed this issue 5 years ago · 5 comments

Hi German,

Alex Seitz had a male patient with a large duplication on chrX, so it was determined to be a female.
Is there a way to overwrite the gender for a sample?

Best,
Marc

The data of the case can be found here: /mnt/users/ahsturm1/Sandbox/ClinCNV/bug_gender_clustering/

Answer 1 · 2019-10-16T12:53:36.000Z

In addition to the large duplication on chrX, this patient also had a large deletion on chrY.

Answer 2 · 2019-10-16T15:38:25.000Z

Large deletion on Y and large duplication on X? Is it truly male? There is no manual assignment of genders, but i may implement it on Friday. This is one in a million case...

>> Marc Sturm ***@***.***> 16.10.19 13:18 >>>

Hi German, Alex Seitz had a **male** patient with a large duplication on chrX, so it was determined to be a **female**. Is there a way to overwrite the gender for a sample? Best, Marc The data of the case can be found here: /mnt/users/ahsturm1/Sandbox/ClinCNV/bug_gender_clustering/

…

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Answer 3 · 2019-10-17T07:18:46.000Z

Hi,
yes, it the patient is definitely male. The sry gene is unaffected.

Best,
Alex

Answer 4 · 2019-10-17T08:52:05.000Z

Yes, you are right. This is a very rare case.
You you should take care of #12 and #13 first.

Answer 5 · 2019-11-29T14:30:02.000Z

I know that it is too late, but now it is possible with --sex flag. There only 2 modifiers are accepted: "M" or "F" (not "male" or any others). Works only if you speciify the sample (so it is still not possible to give a table of sexes for the cohort). Tested and worked.