Unable to locate HMM File for Axiom UKB Array

WGLab / PennCNV

Copy number vaiation detection from SNP arrays

http://penncnv.openbioinformatics.org

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Unable to locate HMM File for Axiom UKB Array #46

Closed npatel22526 closed 5 years ago

npatel22526 commented 5 years ago

Hello,

I am running PennCNV on about 9K samples and noticed that HMM file is not available for Axiom UKB Array. Would it be possible to use "affygw6.hmm" instead ? or the model file has to be generated by "train".

Best, Nick

kaichop commented 5 years ago

sorry that I missed this email. No need to train and you can use the affygw6.hmm. Also check the paper http://www.sciencedirect.com/science/article/pii/S0006322316327111 to see how they used Axiom array.

npatel22526 commented 5 years ago

Thanks for suggestion. That is the paper I followed and they have trained the model using 100 samples but wanted to checked with you as script says "--train train optimized HMM model (not recommended to use)"