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CenterForMedicalGeneticsGhent / WisecondorX

WisecondorX — An evolved WISECONDOR
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cutoffs for gain and loss #87

Closed asaki1986 closed 2 years ago

asaki1986 commented 2 years ago

Hi,

Many thanks for developing such a great tool to analyze the sWGS data.

Rather than NIPT data, we are focusing on the sWGS data from germline blood samples.

Obviously, Z-SCORE of 3 is pre-defined for fetal samples.

Any suggestions for z-score parameter tuning, since the program still output a gain or loss even z-score was set to 7.

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matthdsm commented 2 years ago

Hi,

You can get the raw segments with log2 ratio's by using the --bed flag during the predict step. https://github.com/CenterForMedicalGeneticsGhent/WisecondorX#stage-3-predict-copy-number-alterations

Cheers M

asaki1986 commented 2 years ago

Hi,

You can get the raw segments with log2 ratio's by using the --bed flag during the predict step. https://github.com/CenterForMedicalGeneticsGhent/WisecondorX#stage-3-predict-copy-number-alterations

Cheers M

Thanks,

Sure I can get the raw log2ratio using --bed flag.

So you suggest using raw log2ratio to predict the CNA region other than z score?