Tumor-match mode doubt

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Paulo Ricardo

• August 22, 2024 13:20

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
Can I have a command like this:

My case is inbred mice

-i Tumor.bam

-i normal1.bam

-i normal2.bam

-i normal3.bam

-normal normal1

-normal normal2

-normal normal3

What I mean is that I don't have a match sample. However, since I'm working with inbred mice can I run each tumor sample I have, against all the controls like this?

Thank you for your attention,

Paulo

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  Gökalp Çelik

  • August 23, 2024 11:06

  Hi Paulo Ricardo

  Since the species is inbred this would be a better practice than not having a comparable control for any of those samples. 

  Regards.

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