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bioinform / neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
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Regarding the necessity of normal.bam file #42

Open ghost opened 5 years ago

ghost commented 5 years ago

I am currently working on a tumor bulk RNA-seq data set in order to identify somatic mutations. I have the BAM file for the tumor data set but I do not have the BAM file for a normal sample. Is there any way to use NeuSomatic without a normal BAM file?

amit21AIT commented 5 years ago

Ya same issue .

msahraeian commented 5 years ago

Thanks for your interest in NeuSomatic. Currently, NeuSomatic can only support tumor-normal somatic mutation detection. We plan to extend it to tumor-only mode in near future.

amit21AIT commented 5 years ago

Can you suggest any other tool or technique for somatic mutation detection using tumor - only mode because i don't have the normal.bam file

msahraeian commented 5 years ago

@amit21AIT I guess methods like MuTect2 and VarDict can perform tumor-only calling, although they may have difficulty in filtering some FPs and germline calls without normal match.

ldcato commented 2 years ago

Just wondering if there was an update from the developers on when an extension to tumor-only mode may be available?