Issue Running SomaticCombiner

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2.3 years ago

Emily • 0

Hi!

I have been trying to run this software to combine the mutation calls from software Mutect2 and MuSE from a single sample, but have been running into issues. I checked that both vcfs are not empty. Here is a screenshot of the output. Does anyone know what the warning means? The MuSE VCF defines the tumor and normal sample used to call the somatic mutations.

I would appreciate any help/advice that anyone has to offer. Or, is there another similar tool that I could use instead?

Thanks, Emily screenshot_of_error

somaticcombiner vcf muse mutect2 • 771 views

ADD COMMENT • link updated 2.2 years ago by a.angeles • 0 • written 2.3 years ago by Emily • 0

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Hi! I'm also encountering the same error in somaticCombiner V1.03 using mutect2 and varscan vcfs as input. I wonder if it has something to do with the variations in vcf files produced by different callers. Have you determined what this error message means?

Error: the samples in <sample_name> not equals to 2 or 0! The variants in this file will be skipped!

ADD REPLY • link 2.2 years ago by a.angeles • 0

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