mutect2.bam could not find the mutation, but bqsr found the mutation

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cjz

• December 09, 2021 08:04

I use a bed to find mutations and use the mutect2 process. Normal samples and tumor samples use mutect2 for mutation detection. After importing the bam file of bqsr into IGV, I found that this site has a difference in mutation multiples between normal and tumor samples. But this mutation cannot be found when mutect2.bam is imported into IGV. why？

Then use another bed to find the mutation..it  can be found in mutect2.bam Why is this happening? Both beds contain the location of the mutation

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  Pamela Bretscher

  • December 09, 2021 11:11

  Hi cjz,

  Could you take a look at this troubleshooting document for when Mutect2 does not call an expected variant and see if any of the information and suggestions are useful in your situation?

  Kind regards,

  Pamela

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  ISmolicz

  • April 23, 2023 19:40

  Hi cjz,

  Please may I ask if you managed to resolve the issue described in your initial post above? If so, what was the cause, and please could you advise on how it was resolved?

  Thank you for your time and help.

  Kind regards.

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