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Published 20 hours ago • verified publisher icon bioinform

Regarding the necessity of normal.bam file

Open ghost opened this issue 5 years ago • 5 comments

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?

ghost avatar Jun 20 '19 09:06 ghost

Ya same issue .

amit21AIT avatar Jun 22 '19 08:06 amit21AIT

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.

msahraeian avatar Jun 22 '19 08:06 msahraeian

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

amit21AIT avatar Jun 22 '19 10:06 amit21AIT

@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.

msahraeian avatar Jun 24 '19 18:06 msahraeian

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

ldcato avatar Feb 04 '22 21:02 ldcato