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NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
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truth somatic variant .vcf file #50

Open yueyangtime opened 5 years ago

yueyangtime commented 5 years ago

hi: where can I get the truth somatic variant .vcf file?

sincerely, Yueyang.

msahraeian commented 5 years ago

@yueyangtime hi, would you please explain for which sample you are interested in the truth vcf file?

yueyangtime commented 5 years ago

Hi, For training mode, truth somatic variant .vcf file is needed, is this .vcf document related to the sample to be analyzed? or is this a public file that can be downloaded from the website？

thanks sincerely, Yueyang.

msahraeian commented 5 years ago

@yueyangtime If you want to train NeuSomatic on your sample of interest, you should have a truth .vcf for that sample. We have not released the truth files for our trainings as they are not enough to perform training and you need to have other information like the tumor and normal alignment .bam files for the training samples. We provide a set of trained models used in our paper here. To prepare training data for your samples, you can check here. If you need help on that please let us know.